Structural Basis for Methyl Transfer by a Radical SAM Enzyme
|
|
- Scot Merritt
- 6 years ago
- Views:
Transcription
1 Supporting Online Material for Structural Basis for Methyl Transfer by a Radical SAM Enzyme Amie K. Boal, Tyler L. Grove, Monica I. McLaughlin, Neela H. Yennawar, Squire J. Booker,* Amy C. Rosenzweig* *To whom correspondence should be addressed. squire@psu.edu (S.J.B.); amyr@northwestern.edu (A.C.R.) This PDF file includes: Published 28 April 2011 on Science Express DOI: /science Materials and Methods Figs. S1 to S18 Table S1 References
2 Materials and Methods General crystallographic methods. All datasets were processed using the HKL2000 package (51) and solved by multiple anomalous dispersion (MAD) phasing using SHARP/autoSHARP (52, 53) or by molecular replacement using the program PHASER (54). Model building and refinement were performed with Coot and Refmac5, respectively (55, 56). Data collection and refinement statistics are shown in Table S1. Ramachandran plots were calculated with PROCHECK (57) and MolProbity (58). Diffraction-component precision index (DPI) errors were calculated with SFCHECK (59). Figures were prepared using PyMOL (60) and electrostatic surface potential calculations were performed with the PyMOL APBS plugin (49) at 150 mm monovalent ion concentration. All data were collected at the Life Sciences Collaborative Access Team (LS-CAT) and General Medicine and Cancer Institutes Collaborative Access Team (GM/CA-CAT) beamlines at the Advanced Photon Source. RlmN structure. RlmN from Escherichia coli was prepared as described previously (7) from a construct encoding a C-terminal hexahistidine affinity tag that remains uncleaved after purification. All manipulations were carried out in a Coy anaerobic chamber. Protein solutions (100 mg/ml in 10 mm HEPES ph 7.5, 500 mm KCl, 10% glycerol, 5 mm DTT) were diluted 1:10 in 20 mm HEPES ph 7.6, allowed to stand overnight, and centrifuged at 10,000 g prior to crystallization. Yellow-brown rectangular prism-shaped crystals were obtained using the hanging drop vapor diffusion method at 20 C with 10% (w/v) PEG 6000, 5% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.1 M HEPES ph 7.5 as a precipitant equilibrated against a 0.25 M LiCl well solution. Crystals were soaked in cryoprotectant solution (30% (w/v) glycerol, 10% (w/v) PEG
3 6000, 5% (v/v) MPD, 0.1 M HEPES ph 7.5) for less than 5 min, mounted on rayon loops, and flash cooled in liquid nitrogen. Diffraction data for MAD phasing were collected at the Fe absorption peak and a remote wavelength (Table S1). A high-resolution native data set was also collected. The peak and remote data sets were subjected individually to an initial round of autosharp that yielded the location of the iron-sulfur cluster. High resolution phase information was obtained by placing individual iron atoms within the cluster density using the Fe anomalous Fourier map, a model cluster, and the locations of the three cysteinyl ligands (61). Phasing with SHARP (53) (peak 2 and remote 2 datasets) with the eight iron sites (four sites per cluster, one cluster in each of the two molecules in the ASU) determined as above yielded good quality electron density maps after solvent flattening with SOLOMON (62). An initial model was built automatically using Buccaneer (63). Further adjustment manually with Coot (55) was aided by use of additional data from a second crystal phased as described above, but with a higher resolution native dataset included (peak 1, remote 1, and native 1 datasets). This map showed improved side chain density and was used during manual model building. Non-crystallographic symmetry restraints were used during model building but removed in the later stages of refinement. The final model was refined against the native 1 dataset and consists of residues and for chain A, residues and for chain B, eight iron atoms, eight sulfur atoms, one MPD molecule, and 366 water molecules. Electron density was not observed for residues in chains A and B. Ramachandran plots indicate that 99.9% of the residues are in the allowed and additionally allowed regions. The DPI error is Å.
4 RlmN+SAM structure. RlmN crystals obtained as described above were soaked in mother liquor containing 1 mm S-adenosyl-L-methionine (SAM) for 45 min in a Coy anaerobic chamber. Crystals were briefly transferred to cryoprotectant solution (30% (v/v) PEG 400, 10% (w/v) PEG 6000, 5% (v/v) MPD, 0.1 M HEPES ph 7.5), then mounted on rayon loops and flash frozen in liquid nitrogen. The structure was solved by molecular replacement using the coordinates of RlmN as a starting model. The final model consists of residues for chain A, residues for chain B, eight iron atoms, eight sulfur atoms, two SAM molecules, and 181 water molecules. Electron density was not observed beyond residue 349 in chain A. Ramachandran plots indicate that 100% of the residues are in the allowed and additionally allowed regions. The DPI error is Å.
5 Figure S1. The methylation reactions catalyzed by E. coli RlmN and S. aureus Cfr (7). RlmN methylates the C2 position of A2503. Cfr catalyzes methylation of C2 and C8, but C8 is the primary target.
6 Figure S2. The proposed mechanism for C2 methylation of A2503 by RlmN (7).
7 Figure S3. Secondary structure matching (SSM) superposition (PDBeFold server (64)) of the E. coli RlmN (purple) α 6 /β 6 core with the PFL-AE (PDB accession code 3CB8) core structure (30). Two views are shown, (A) and (B). The [4Fe-4S] cluster is shown as a space filling model in orange (iron) and yellow (sulfur) and the SAM cosubstrate is shown in stick format (green) and colored by atom type. The rmsd is 2.6 Å for 220 Cα atoms. The most significant differences between the two structures are found in the indicated loops connecting core secondary structure elements. The equivalent to loop C, located between β6 and α6, is shorter in RlmN and lacks the helical region. The loop between α1 and β2 is longer in RlmN and is located on the same side of the barrel as a loop in PFL-AE (not shown) that undergoes dramatic conformational change upon binding of a substrate analog (30). The structural differences in these loops may reflect differences in substrate specificity for the two enzymes.
8 Figure S4. Structure-based sequence alignment of the RlmN N-terminal domain with a representative HhH 2 structure (RuvA, PDB accession code 2C7Y). The fold is defined by a set of conserved hydrophobic residues contributed by each helix (bottom, black bars) and a GXG sequence conserved in the two hairpin regions (bottom, orange bars) (36). The paired GXG sequences typically confer sequence independent minor-groove recognition of B-form DNA through interaction with the phosphate backbone on both strands (36). In the RlmN domain, lack of conservation of the hairpin sequence and deviation from a pseudosymmetric arrangement of HhH motifs may result in specificity for an RNA structure. Similar deviations are observed in a domain found in DNA polymerase β which interacts with only one DNA strand (65).
9 Figure S5. The α1/β2 loop adopts different conformations and engages in crystal contacts. (A) Residues shown in stick format (RlmN structure, chain B). The β7 extension is shown in blue, the α 6 /β 6 core in purple, the β 1-3 extension in pink, and the N-terminal domain in green. In this molecule, the loop packs against a portion of the second molecule in the ASU, placing it close to the β 1-3 extension. (B) and (C) show an overlay of the three conformations observed in the four molecules from the two structures.
10 Figure S6. The C-terminal helix in the RlmN+SAM structure. (A) 2F o -F c (1.3σ) map of residues in chain B. (B) and (C) show interactions with a symmetry related molecule. The C- terminal helix also interacts in an intramolecular fashion with a short loop composed of residues (D-F) show zoomed-in views of hydrophobic (D) and hydrogen bonding interactions (E) with the symmetry related molecule (D and E) and residues from the same molecule (F). The side chain density is more pronounced for the residues that engage in specific hydrophobic or hydrogen bonding interactions. The intramolecular interactions shown in view (F) are not observed in the absence of SAM because the helix is shifted away from the core. Notably, the residues that comprise this helix are absent in Cfr.
11 Figure S7. The iron-sulfur cluster in RlmN and RlmN+SAM. 2F o -F c electron density map (1.5σ) for the side chains of residues 125, 129, and 132 within the CX 3 CX 2 C motif, the [4Fe-4S] cluster, and the SAM cofactor in the RlmN+SAM structure. The SAM methionine sulfur atom is located 3.7 Å from the two nearest sulfur atoms in the [4Fe-4S] cluster and 3.2 Å from the unique iron site. These distances are consistent with other structurally characterized radical SAM enzymes (39). In the inset, an Fe edge anomalous difference electron density map (9.0σ) for the RlmN structure shows full occupancy of all four iron atoms in the cluster.
12 Figure S8. A hydrogen bonding network between SAM (shown as sticks, green), the α 6 /β 6 core, residues (colored as in Fig. 1), and ordered solvent (red spheres). Additionally, Glu 105 forms hydrogen bonds to the backbone of the linker region. These interactions may trigger ordering of residues upon SAM binding. The use of water-mediated contacts may be an especially important feature of this network, allowing for controlled repositioning of the loop within the active site.
13 Figure S9. Overlay of the RlmN (light gray) and RlmN+SAM structures (colored as in Fig. 1). (A) A view of the entire structure. Areas that undergo large changes are indicated by black arrows. The C-terminal helix (blue) experiences a significant positional shift due to ordering of residues (B) A zoomed-in view of the SAM binding site. Conserved residue Asn 312 shifts 2.5 Å (Cα) to fold over the face of the SAM adenine moiety. (C) Loops near the active site shift position or become ordered (black arrows) upon SAM binding resulting in a less solvent exposed active site at the C-terminal end of the barrel. Similar ordering phenomena and conformational changes are observed upon substrate binding in other RS enzymes (30) and are proposed to prevent unwanted chemistry such as abortive cleavage of SAM.
14 Figure S10. 2F o -F c electron density map (1.0σ) for residues in the RlmN+SAM structure. Weak electron density is observed for two residues (Ala 353 and Gly 360), labeled with asterisks, suggesting conformational flexibility.
15 Figure S11. A stereoview of the active site of RlmN.
16 Figure S12. Active site overlay of RlmN+SAM with RlmN (white). Cys 118 changes rotamer upon SAM binding, inducing a flip in the Met 176-Gly 177 peptide bond (or vice versa). This may result in stabilization of the SAM-bound state and favorable positioning of the Met 176 backbone carbonyl and Cys 118 side chain for various steps in the reaction pathway. The location of the Met 176 side chain methyl group, 4 Å from the site of 5 -da formation, may be important in controlling access to the reactive site.
17 Figure S13. Methyl acquistion by Cys 355 may occur via SAM bound to the [4Fe-4S] cluster. (A) The mcys 355 sulfur atom is positioned favorably to be deprotonated by nearby strictly conserved residue Glu 105 (perhaps via a local water network) and to subsequently attack the carbon atom of the SAM methyl substituent. (B) Local hydrogen bonding interactions may be altered in the presence of unmethylated Cys 355 to further facilitate methyl transfer or downstream reaction steps.
18 Figure S14. Comparison of the RlmN+SAM structure (colored as in Fig. 1) and the PFL- AE+peptide substrate (yellow) structure (30) (PDB accession code 3CB8). (A) Side-by-side view showing that the general location of the peptide substrate in the PFL-AE complex structure is similar to that of residues in RlmN+SAM. This observation is notable since these enzymes both form a protein centered radical in these regions upon 5 -da generation in the active site. (B) Side-by-side view showing that the PFL peptide glycyl radical site (Gly 734) (right) is shifted toward the 5 carbon (*) of the SAM cofactor compared to the position of the methyl substituent on mcys 355 in RlmN+SAM (left). An important structural feature of the loop may be the exposure of backbone carbonyls (such as that of Gly 734, shown) to interact with the SAM cosubstrate. Similar interactions may guide positioning of mcys 355 in RlmN upon substrate binding. (C) A manual alignment of the backbone atoms in the PFL-AE substrate and RlmN residues shows a similar finger loop structure perhaps defined by a potential hydrogen bonding interaction indicated by the gray dashed line. The site of radical formation in RlmN (mcys 355) does not align here with the glycyl radical site in PFL (Gly 734). It aligns with an adjacent serine, suggesting the site of reactivity is not controlled by the sequence of the loop but instead by its precise location in the active site. In each system, distal structural elements in the enzyme/substrate complex may ultimately control the position of the loop.
19 Figure S15. An additional view in the comparison of the electrostatic surface potential (A) in RlmN to a sequence conservation map from pairwise alignment of E. coli RlmN and S. aureus Cfr (B) as shown in Figure 3.
20 Figure S16. Sequence conservation near the active site in a pairwise alignment of E. coli RlmN and S. aureus Cfr. (A) shows strictly conserved residues in orange, neutral substitutions in tan, and variable regions in white. The surface near mcys 355 and Cys 118, residues identified as mechanistically critical, is highly conserved in both enzymes. (B) is colored as in Fig. 1. Specific residues substituted in Cfr are shown in stick format and labeled in black. Several relatively conservative substitions (Thr, Val in RlmN to Ser in Cfr) may subtly alter hydrogen bonding patterns to promote substrate conformational changes. A salt bridge between conserved residue Arg 344 and Glu 278 (Ala in Cfr) could be an important factor in substrate orientation within the RlmN active site.
21 Figure S17. Surface map (ConSURF server) (66) of sequence conservation among the entire RlmN/Cfr family of enzymes (700 sequences) (8). Views in (A), (B), and (C) are as shown in Figs. 3A-D, and S15.
22 Figure S18. Overlay of a Cfr homology model (I-TASSER server) (67) (tan) onto the RlmN+SAM structure (colored as in Fig. 1). Brackets denote large structural insertions found in RlmN.
23 Table S1. Data collection and refinement statistics. Data collection Wavelength (Å) RlmN Native 1 1 RlmN Peak 1 1 RlmN Remote 1 1 RlmN Peak 2 2 RlmN RlmN+SAM 1 Remote Space group C222 1 P Cell dimensions a, b, c (Å) 72.15, 80.41, , 80.46, ( ) (0.412) 72.19, 80.42, ( ) (0.488) 72.14, 80.33, ( ) (0.645) 72.24, 80.43, ( ) (0.688) 55.18, 55.62, Resolution (Å) ( ) ( ) R sym or R merge (0.529) (0.507) <I /σi> 23.9 (2.1) 26.0 (5.1) 20.3 (2.4) 32.2 (7.1) 23.6 (4.3) 16.5 (2.0) Completeness 99.3 (92.3) (99.7) 98.1 (82.9) (95.1) (%) (99.8) (99.9) Redundancy 7.0 (4.4) 13.2 (7.8) 12.3 (4.1) 28.5 (24.5) 14.1 (11.9) 4.9 (3.6) Refinement Resolution (Å) No. reflections R work / R free 0.213/ /0.242 No. atoms Protein Ligand/ion Water B-factors (Å 2 ) Protein Ligand/ion Water R.m.s. deviations Bond lengths (Å) Bond angles ( ) Data collected at LS-CAT beamlines 21-ID-D, 21-ID-G, 21-ID-F 2 Data collected at GM/CA-CAT beamline 23-ID-D
24 References 51. Z. Otwinowski, W. Minor, Methods Enzymol. 276, 307 (1997). 52. C. Vonrhein, E. Blanc, P. Roversi, G. Bricogne, in Methods in Molecular Biology, S. Doublié, Ed. (Humana Press, Inc., Totowa, NJ, 2007), vol. 364, pp E. de la Fortelle, G. Bricogne, Methods Enzymol. 276, 472 (1997). 54. A. J. McCoy, R. W. Grosse-Kunstleve, L. C. Storoni, R. J. Read, Acta Cryst. D61, 458 (2005). 55. P. Emsley, K. Cowtan, Acta Cryst. D60, 2126 (2004). 56. G. N. Murshudov, A. A. Vagin, E. J. Dodson, Acta Cryst. D53, 240 (1997). 57. R. A. Laskowski, J. Appl. Cryst. 26, 283 (1993). 58. V. B. Chen et al., Acta Cryst. D66, 12 (2010). 59. A. A. Vaguine, J. Richelle, S. J. Wodak, Acta Cryst. D55, 191 (1999). 60. W. L. Delano, The PyMOL molecular graphics system. (DeLano Scientific, San Carlos, CA, 2002). 61. J. W. Peters, H. D. Bellamy, J. Appl. Cryst. 32, 1180 (1999). 62. J. P. Abrahams, A. G. W. Leslie, Acta Cryst. D52, 30 (1996). 63. K. Cowtan, Acta Cryst. D62, 1002 (2006). 64. E. Krissinel, K. Henrick, Acta Cryst. D60, 2256 (2004). 65. M. R. Sawaya, R. Prasad, S. H. Wilson, J. Kraut, H. Pelletier, Biochemistry 36, (1997). 66. M. Landau et al., Nucleic Acids Res. 33, W299 (2005). 67. A. Roy, A. Kucukural, Y. Zhang, Nat. Protoc. 5, 725 (2010).
SUPPLEMENTARY INFORMATION
Supplementary Results DNA binding property of the SRA domain was examined by an electrophoresis mobility shift assay (EMSA) using synthesized 12-bp oligonucleotide duplexes containing unmodified, hemi-methylated,
More informationNew Delhi Metallo-β-Lactamase: Structural Insights into β- Lactam Recognition and Inhibition
Supporting Information New Delhi Metallo-β-Lactamase: Structural Insights into β- Lactam Recognition and Inhibition Dustin T. King, Liam J. Worrall, Robert Gruninger, Natalie C.J. Strynadka* AUTHOR ADDRESS:
More informationNitrogenase MoFe protein from Clostridium pasteurianum at 1.08 Å resolution: comparison with the Azotobacter vinelandii MoFe protein
Acta Cryst. (2015). D71, 274-282, doi:10.1107/s1399004714025243 Supporting information Volume 71 (2015) Supporting information for article: Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08
More informationSUPPLEMENTARY INFORMATION
Table of Contents Page Supplementary Table 1. Diffraction data collection statistics 2 Supplementary Table 2. Crystallographic refinement statistics 3 Supplementary Fig. 1. casic1mfc packing in the R3
More informationElectronic Supplementary Information (ESI) for Chem. Commun. Unveiling the three- dimensional structure of the green pigment of nitrite- cured meat
Electronic Supplementary Information (ESI) for Chem. Commun. Unveiling the three- dimensional structure of the green pigment of nitrite- cured meat Jun Yi* and George B. Richter- Addo* Department of Chemistry
More informationSupporting Information. Synthesis of Aspartame by Thermolysin : An X-ray Structural Study
Supporting Information Synthesis of Aspartame by Thermolysin : An X-ray Structural Study Gabriel Birrane, Balaji Bhyravbhatla, and Manuel A. Navia METHODS Crystallization. Thermolysin (TLN) from Calbiochem
More informationTable 1. Crystallographic data collection, phasing and refinement statistics. Native Hg soaked Mn soaked 1 Mn soaked 2
Table 1. Crystallographic data collection, phasing and refinement statistics Native Hg soaked Mn soaked 1 Mn soaked 2 Data collection Space group P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 Cell
More informationStructure and evolution of the spliceosomal peptidyl-prolyl cistrans isomerase Cwc27
Acta Cryst. (2014). D70, doi:10.1107/s1399004714021695 Supporting information Volume 70 (2014) Supporting information for article: Structure and evolution of the spliceosomal peptidyl-prolyl cistrans isomerase
More informationSupplementary materials. Crystal structure of the carboxyltransferase domain. of acetyl coenzyme A carboxylase. Department of Biological Sciences
Supplementary materials Crystal structure of the carboxyltransferase domain of acetyl coenzyme A carboxylase Hailong Zhang, Zhiru Yang, 1 Yang Shen, 1 Liang Tong Department of Biological Sciences Columbia
More informationPathogenic C9ORF72 Antisense Repeat RNA Forms a Double Helix with Tandem C:C Mismatches
Supporting Information Pathogenic C9ORF72 Antisense Repeat RNA Forms a Double Helix with Tandem C:C Mismatches David W. Dodd, Diana R. Tomchick, David R. Corey, and Keith T. Gagnon METHODS S1 RNA synthesis.
More informationTable S1. Overview of used PDZK1 constructs and their binding affinities to peptides. Related to figure 1.
Table S1. Overview of used PDZK1 constructs and their binding affinities to peptides. Related to figure 1. PDZK1 constru cts Amino acids MW [kda] KD [μm] PEPT2-CT- FITC KD [μm] NHE3-CT- FITC KD [μm] PDZK1-CT-
More informationSUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature11524 Supplementary discussion Functional analysis of the sugar porter family (SP) signature motifs. As seen in Fig. 5c, single point mutation of the conserved
More informationSupplementary Figure 1. Aligned sequences of yeast IDH1 (top) and IDH2 (bottom) with isocitrate
SUPPLEMENTARY FIGURE LEGENDS Supplementary Figure 1. Aligned sequences of yeast IDH1 (top) and IDH2 (bottom) with isocitrate dehydrogenase from Escherichia coli [ICD, pdb 1PB1, Mesecar, A. D., and Koshland,
More informationSupplemental Data. Structure of the Rb C-Terminal Domain. Bound to E2F1-DP1: A Mechanism. for Phosphorylation-Induced E2F Release
Supplemental Data Structure of the Rb C-Terminal Domain Bound to E2F1-DP1: A Mechanism for Phosphorylation-Induced E2F Release Seth M. Rubin, Anne-Laure Gall, Ning Zheng, and Nikola P. Pavletich Section
More informationSupporting Information
Supporting Information Structural Basis of the Antiproliferative Activity of Largazole, a Depsipeptide Inhibitor of the Histone Deacetylases Kathryn E. Cole 1, Daniel P. Dowling 1,2, Matthew A. Boone 3,
More informationIntroduction to Comparative Protein Modeling. Chapter 4 Part I
Introduction to Comparative Protein Modeling Chapter 4 Part I 1 Information on Proteins Each modeling study depends on the quality of the known experimental data. Basis of the model Search in the literature
More informationSUPPLEMENTARY INFORMATION
Supplementary materials Figure S1 Fusion protein of Sulfolobus solfataricus SRP54 and a signal peptide. a, Expression vector for the fusion protein. The signal peptide of yeast dipeptidyl aminopeptidase
More informationActa Crystallographica Section F
Supporting information Acta Crystallographica Section F Volume 70 (2014) Supporting information for article: Chemical conversion of cisplatin and carboplatin with histidine in a model protein crystallised
More informationModel Mélange. Physical Models of Peptides and Proteins
Model Mélange Physical Models of Peptides and Proteins In the Model Mélange activity, you will visit four different stations each featuring a variety of different physical models of peptides or proteins.
More informationSUPPLEMENTARY INFORMATION
Dph2 SeMet (iron-free) # Dph2 (iron-free) Dph2-[4Fe-4S] Data collection Space group P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 Cell dimensions a, b, c (Å) 58.26, 82.08, 160.42 58.74, 81.87, 160.01 55.70, 80.53,
More informationDiphthamide biosynthesis requires a radical iron-sulfur enzyme. Pennsylvania State University, University Park, Pennsylvania 16802, USA
Diphthamide biosynthesis requires a radical iron-sulfur enzyme Yang Zhang, 1,4 Xuling Zhu, 1,4 Andrew T. Torelli, 1 Michael Lee, 2 Boris Dzikovski, 1 Rachel Koralewski, 1 Eileen Wang, 1 Jack Freed, 1 Carsten
More informationSUPPLEMENTARY INFORMATION
Fig. 1 Influences of crystal lattice contacts on Pol η structures. a. The dominant lattice contact between two hpol η molecules (silver and gold) in the type 1 crystals. b. A close-up view of the hydrophobic
More informationSUPPLEMENTARY FIGURES
SUPPLEMENTARY FIGURES Supplementary Figure 1 Protein sequence alignment of Vibrionaceae with either a 40-residue insertion or a 44-residue insertion. Identical residues are indicated by red background.
More informationPhysiochemical Properties of Residues
Physiochemical Properties of Residues Various Sources C N Cα R Slide 1 Conformational Propensities Conformational Propensity is the frequency in which a residue adopts a given conformation (in a polypeptide)
More informationPacking of Secondary Structures
7.88 Lecture Notes - 4 7.24/7.88J/5.48J The Protein Folding and Human Disease Professor Gossard Retrieving, Viewing Protein Structures from the Protein Data Base Helix helix packing Packing of Secondary
More informationHigh-resolution crystal structure of ERAP1 with bound phosphinic transition-state analogue inhibitor
High-resolution crystal structure of ERAP1 with bound phosphinic transition-state analogue inhibitor Petros Giastas 1, Margarete Neu 2, Paul Rowland 2, and Efstratios Stratikos 1 1 National Center for
More informationViewing and Analyzing Proteins, Ligands and their Complexes 2
2 Viewing and Analyzing Proteins, Ligands and their Complexes 2 Overview Viewing the accessible surface Analyzing the properties of proteins containing thousands of atoms is best accomplished by representing
More informationSUPPLEMENTARY INFORMATION
Supplementary Table 1: Data collection, phasing and refinement statistics ChbC/Ta 6 Br 12 Native ChbC Data collection Space group P4 3 2 1 2 P4 3 2 1 2 Cell dimensions a, c (Å) 132.75, 453.57 132.81, 452.95
More informationSUPPLEMENTARY INFORMATION. doi: /nature07461
Figure S1 Electrophysiology. a ph-activation of. Two-electrode voltage clamp recordings of Xenopus oocytes expressing in comparison to waterinjected oocytes. Currents were recorded at 40 mv. The ph of
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Jan 14, 2019 11:10 AM EST PDB ID : 6GYW Title : Crystal structure of DacA from Staphylococcus aureus Authors : Tosi, T.; Freemont, P.S.; Grundling, A. Deposited
More informationActa Crystallographica Section D
Supporting information Acta Crystallographica Section D Volume 70 (2014) Supporting information for article: Structural characterization of the virulence factor Nuclease A from Streptococcus agalactiae
More informationSupplementary figure 1. Comparison of unbound ogm-csf and ogm-csf as captured in the GIF:GM-CSF complex. Alignment of two copies of unbound ovine
Supplementary figure 1. Comparison of unbound and as captured in the GIF:GM-CSF complex. Alignment of two copies of unbound ovine GM-CSF (slate) with bound GM-CSF in the GIF:GM-CSF complex (GIF: green,
More informationStructurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
Supplementary Information to Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis Matthew J. Rodrigues 1,2, Volker Windeisen 1,3, Yang Zhang 4, Gabriela Guédez 3, Stefan
More informationNature Structural and Molecular Biology: doi: /nsmb.2938
Supplementary Figure 1 Characterization of designed leucine-rich-repeat proteins. (a) Water-mediate hydrogen-bond network is frequently visible in the convex region of LRR crystal structures. Examples
More informationIntroduction to" Protein Structure
Introduction to" Protein Structure Function, evolution & experimental methods Thomas Blicher, Center for Biological Sequence Analysis Learning Objectives Outline the basic levels of protein structure.
More informationRanjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India. 1 st November, 2013
Hydration of protein-rna recognition sites Ranjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India 1 st November, 2013 Central Dogma of life DNA
More informationSUPPLEMENTARY INFORMATION
doi:10.1038/nature11085 Supplementary Tables: Supplementary Table 1. Summary of crystallographic and structure refinement data Structure BRIL-NOP receptor Data collection Number of crystals 23 Space group
More informationThe structure of a nucleolytic ribozyme that employs a catalytic metal ion. Yijin Liu, Timothy J. Wilson and David M.J. Lilley
SUPPLEMENTARY INFORMATION The structure of a nucleolytic ribozyme that employs a catalytic metal ion Yijin Liu, Timothy J. Wilson and David M.J. Lilley Cancer Research UK Nucleic Acid Structure Research
More informationProtein Dynamics. The space-filling structures of myoglobin and hemoglobin show that there are no pathways for O 2 to reach the heme iron.
Protein Dynamics The space-filling structures of myoglobin and hemoglobin show that there are no pathways for O 2 to reach the heme iron. Below is myoglobin hydrated with 350 water molecules. Only a small
More informationSUPPLEMENTARY INFORMATION
Supplementary Table 1: Amplitudes of three current levels. Level 0 (pa) Level 1 (pa) Level 2 (pa) TrkA- TrkH WT 200 K 0.01 ± 0.01 9.5 ± 0.01 18.7 ± 0.03 200 Na * 0.001 ± 0.01 3.9 ± 0.01 12.5 ± 0.03 200
More informationSUPPLEMENTARY INFORMATION
doi:10.1038/nature11054 Supplementary Fig. 1 Sequence alignment of Na v Rh with NaChBac, Na v Ab, and eukaryotic Na v and Ca v homologs. Secondary structural elements of Na v Rh are indicated above the
More informationSUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature11744 Supplementary Table 1. Crystallographic data collection and refinement statistics. Wild-type Se-Met-BcsA-B SmCl 3 -soaked EMTS-soaked Data collection Space
More informationSupporting Information
Supporting Information Ottmann et al. 10.1073/pnas.0907587106 Fig. S1. Primary structure alignment of SBT3 with C5 peptidase from Streptococcus pyogenes. The Matchmaker tool in UCSF Chimera (http:// www.cgl.ucsf.edu/chimera)
More informationDetailed description of overall and active site architecture of PPDC- 3dThDP, PPDC-2HE3dThDP, PPDC-3dThDP-PPA and PPDC- 3dThDP-POVA
Online Supplemental Results Detailed description of overall and active site architecture of PPDC- 3dThDP, PPDC-2HE3dThDP, PPDC-3dThDP-PPA and PPDC- 3dThDP-POVA Structure solution and overall architecture
More informationIgE binds asymmetrically to its B cell receptor CD23
Supplementary Information IgE binds asymmetrically to its B cell receptor CD23 Balvinder Dhaliwal 1*, Marie O. Y. Pang 2, Anthony H. Keeble 2,3, Louisa K. James 2,4, Hannah J. Gould 2, James M. McDonnell
More informationSupporting Information
Supporting Information Horne et al. 10.1073/pnas.0902663106 SI Materials and Methods Peptide Synthesis. Protected 3 -amino acids were purchased from PepTech. Cyclically constrained -residues, Fmoc-ACPC
More informationBiomolecules: lecture 10
Biomolecules: lecture 10 - understanding in detail how protein 3D structures form - realize that protein molecules are not static wire models but instead dynamic, where in principle every atom moves (yet
More informationSUPPLEMENTARY INFORMATION
www.nature.com/nature 1 Figure S1 Sequence alignment. a Structure based alignment of the plgic of E. chrysanthemi (ELIC), the acetylcholine binding protein from the snail Lymnea stagnalis (AchBP, PDB code
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 14, 2018 02:00 pm GMT PDB ID : 3RRQ Title : Crystal structure of the extracellular domain of human PD-1 Authors : Lazar-Molnar, E.; Ramagopal, U.A.; Nathenson,
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Jan 28, 2019 11:10 AM EST PDB ID : 6A5H Title : The structure of [4+2] and [6+4] cyclase in the biosynthetic pathway of unidentified natural product Authors
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 8, 2018 06:13 pm GMT PDB ID : 5G5C Title : Structure of the Pyrococcus furiosus Esterase Pf2001 with space group C2221 Authors : Varejao, N.; Reverter,
More informationRadical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism
SUPPLEMENTARY INFORMATION for: Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism Daniel P. Dowling 1,2, Nathan A. Bruender 3, Anthony P. Young 3, Reid M. McCarty 3,
More informationSupporting Information
Supporting Information Micelle-Triggered b-hairpin to a-helix Transition in a 14-Residue Peptide from a Choline-Binding Repeat of the Pneumococcal Autolysin LytA HØctor Zamora-Carreras, [a] Beatriz Maestro,
More informationSUPPLEMENTARY INFORMATION
doi:10.1038/nature12045 Supplementary Table 1 Data collection and refinement statistics. Native Pt-SAD X-ray source SSRF BL17U SPring-8 BL41XU Wavelength (Å) 0.97947 1.07171 Space group P2 1 2 1 2 1 P2
More informationSupersecondary Structures (structural motifs)
Supersecondary Structures (structural motifs) Various Sources Slide 1 Supersecondary Structures (Motifs) Supersecondary Structures (Motifs): : Combinations of secondary structures in specific geometric
More informationCatalytic Mechanism of the Glycyl Radical Enzyme 4-Hydroxyphenylacetate Decarboxylase from Continuum Electrostatic and QC/MM Calculations
Catalytic Mechanism of the Glycyl Radical Enzyme 4-Hydroxyphenylacetate Decarboxylase from Continuum Electrostatic and QC/MM Calculations Supplementary Materials Mikolaj Feliks, 1 Berta M. Martins, 2 G.
More informationSupplemental Information
Supplemental Information Combinatorial Readout of Unmodified H3R2 and Acetylated H3K14 by the Tandem PHD Finger of MOZ Reveals a Regulatory Mechanism for HOXA9 Transcription Yu Qiu 1, Lei Liu 1, Chen Zhao
More informationRational Design of Thermodynamic and Kinetic Binding Profiles by. Optimizing Surface Water Networks Coating Protein Bound Ligands
SUPPORTING INFORMATION Rational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein Bound Ligands Stefan G. Krimmer,, Jonathan Cramer,, Michael Betz,
More informationCHAPTER 29 HW: AMINO ACIDS + PROTEINS
CAPTER 29 W: AMI ACIDS + PRTEIS For all problems, consult the table of 20 Amino Acids provided in lecture if an amino acid structure is needed; these will be given on exams. Use natural amino acids (L)
More informationProtein Structure. W. M. Grogan, Ph.D. OBJECTIVES
Protein Structure W. M. Grogan, Ph.D. OBJECTIVES 1. Describe the structure and characteristic properties of typical proteins. 2. List and describe the four levels of structure found in proteins. 3. Relate
More informationSUPPLEMENTARY INFORMATION
doi:10.1038/nature10955 Supplementary Figures Supplementary Figure 1. Electron-density maps and crystallographic dimer structures of the motor domain. (a f) Stereo views of the final electron-density maps
More informationSupporting Information
Supporting Information Structural Analysis of the Binding of Type I, I 1/2, and II Inhibitors to Eph Tyrosine Kinases Jing Dong, *1 Hongtao Zhao, 1 Ting Zhou, 1 Dimitrios Spiliotopoulos, 1 Chitra Rajendran,
More informationBacterial protease uses distinct thermodynamic signatures for substrate recognition
Bacterial protease uses distinct thermodynamic signatures for substrate recognition Gustavo Arruda Bezerra, Yuko Ohara-Nemoto, Irina Cornaciu, Sofiya Fedosyuk, Guillaume Hoffmann, Adam Round, José A. Márquez,
More informationSupplementary Figure 3 a. Structural comparison between the two determined structures for the IL 23:MA12 complex. The overall RMSD between the two
Supplementary Figure 1. Biopanningg and clone enrichment of Alphabody binders against human IL 23. Positive clones in i phage ELISA with optical density (OD) 3 times higher than background are shown for
More informationDetails of Protein Structure
Details of Protein Structure Function, evolution & experimental methods Thomas Blicher, Center for Biological Sequence Analysis Anne Mølgaard, Kemisk Institut, Københavns Universitet Learning Objectives
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 8, 2018 08:34 pm GMT PDB ID : 1RUT Title : Complex of LMO4 LIM domains 1 and 2 with the ldb1 LID domain Authors : Deane, J.E.; Ryan, D.P.; Maher, M.J.;
More informationPAN-modular Structure of Parasite Sarcocystis muris Microneme Protein SML-2 at 1.95 Å Resolution and the Complex with 1-Thio-β-D-Galactose
Supplementary Material to the paper: PAN-modular Structure of Parasite Sarcocystis muris Microneme Protein SML-2 at 1.95 Å Resolution and the Complex with 1-Thio-β-D-Galactose Jürgen J. Müller, a Manfred
More informationNature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Crystallization. a, Crystallization constructs of the ET B receptor are shown, with all of the modifications to the human wild-type the ET B receptor indicated. Residues interacting
More informationSupporting Information
Supporting Information Naganuma et al. 10.1073/pnas.0901572106 SI Text The Recognition of Ala-SA. Ala-SA is a nonhydrolyzable analog of alanyl-adenylate and is a potent inhibitor of AlaRS (1). The recognition
More informationThe structure of a nucleolytic ribozyme that employs a catalytic metal ion Liu, Yijin; Wilson, Timothy; Lilley, David
University of Dundee The structure of a nucleolytic ribozyme that employs a catalytic metal ion Liu, Yijin; Wilson, Timothy; Lilley, David Published in: Nature Chemical Biology DOI: 10.1038/nchembio.2333
More informationtype GroEL-GroES complex. Crystals were grown in buffer D (100 mm HEPES, ph 7.5,
Supplementary Material Supplementary Materials and Methods Structure Determination of SR1-GroES-ADP AlF x SR1-GroES-ADP AlF x was purified as described in Materials and Methods for the wild type GroEL-GroES
More informationProgramme Last week s quiz results + Summary Fold recognition Break Exercise: Modelling remote homologues
Programme 8.00-8.20 Last week s quiz results + Summary 8.20-9.00 Fold recognition 9.00-9.15 Break 9.15-11.20 Exercise: Modelling remote homologues 11.20-11.40 Summary & discussion 11.40-12.00 Quiz 1 Feedback
More informationSUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis Sergio de Cima, Luis M. Polo, Carmen Díez-Fernández, Ana I. Martínez, Javier
More informationSunhats for plants. How plants detect dangerous ultraviolet rays
Sunhats for plants How plants detect dangerous ultraviolet rays Anyone who has ever suffered sunburn will know about the effects of too much ultraviolet (UV) radiation, in particular UV-B (from 280-315
More informationLecture 12. Metalloproteins - II
Lecture 12 Metalloproteins - II Metalloenzymes Metalloproteins with one labile coordination site around the metal centre are known as metalloenzyme. As with all enzymes, the shape of the active site is
More informationSupporting Information. UV-induced ligand exchange in MHC class I protein crystals
Supporting Information for the article entitled UV-induced ligand exchange in MHC class I protein crystals by Patrick H.N. Celie 1, Mireille Toebes 2, Boris Rodenko 3, Huib Ovaa 3, Anastassis Perrakis
More informationDATE A DAtabase of TIM Barrel Enzymes
DATE A DAtabase of TIM Barrel Enzymes 2 2.1 Introduction.. 2.2 Objective and salient features of the database 2.2.1 Choice of the dataset.. 2.3 Statistical information on the database.. 2.4 Features....
More informationEsser et al. Crystal Structures of R. sphaeroides bc 1
Esser et al. Crystal Structures of R. sphaeroides bc Supplementary Information Trivariate Gaussian Probability Analysis The superposition of six structures results in sextets of 3D coordinates for every
More informationPrediction and refinement of NMR structures from sparse experimental data
Prediction and refinement of NMR structures from sparse experimental data Jeff Skolnick Director Center for the Study of Systems Biology School of Biology Georgia Institute of Technology Overview of talk
More informationSupplementary Information
Supplementary Information The direct role of selenocysteine in [NiFeSe] hydrogenase maturation and catalysis Marta C. Marques a, Cristina Tapia b, Oscar Gutiérrez-Sanz b, Ana Raquel Ramos a, Kimberly L.
More informationSI Text S1 Solution Scattering Data Collection and Analysis. SI references
SI Text S1 Solution Scattering Data Collection and Analysis. The X-ray photon energy was set to 8 kev. The PILATUS hybrid pixel array detector (RIGAKU) was positioned at a distance of 606 mm from the sample.
More informationProcheck output. Bond angles (Procheck) Structure verification and validation Bond lengths (Procheck) Introduction to Bioinformatics.
Structure verification and validation Bond lengths (Procheck) Introduction to Bioinformatics Iosif Vaisman Email: ivaisman@gmu.edu ----------------------------------------------------------------- Bond
More informationIt s the amino acids!
Catalytic Mechanisms HOW do enzymes do their job? Reducing activation energy sure, but HOW does an enzyme catalysis reduce the energy barrier ΔG? Remember: The rate of a chemical reaction of substrate
More informationBioinformatics. Macromolecular structure
Bioinformatics Macromolecular structure Contents Determination of protein structure Structure databases Secondary structure elements (SSE) Tertiary structure Structure analysis Structure alignment Domain
More informationDirect Method. Very few protein diffraction data meet the 2nd condition
Direct Method Two conditions: -atoms in the structure are equal-weighted -resolution of data are higher than the distance between the atoms in the structure Very few protein diffraction data meet the 2nd
More informationSupplementary information
Supplementary information The structural basis of modularity in ECF-type ABC transporters Guus B. Erkens 1,2, Ronnie P-A. Berntsson 1,2, Faizah Fulyani 1,2, Maria Majsnerowska 1,2, Andreja Vujičić-Žagar
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Jan 17, 2019 09:42 AM EST PDB ID : 6D3Z Title : Protease SFTI complex Authors : Law, R.H.P.; Wu, G. Deposited on : 2018-04-17 Resolution : 2.00 Å(reported)
More informationChapter 9 DNA recognition by eukaryotic transcription factors
Chapter 9 DNA recognition by eukaryotic transcription factors TRANSCRIPTION 101 Eukaryotic RNA polymerases RNA polymerase RNA polymerase I RNA polymerase II RNA polymerase III RNA polymerase IV Function
More informationHigh Pressure Freezing. Philippe Carpentier,
High Pressure Freezing Philippe Carpentier, - The system - The method - Some typical examples ESRF Users Meeting 2015: Meeting of MX BAG Representatives and Beamline Staff, 9 th February 2015 Page 1 INTRODUCTION
More informationStructure, mechanism and ensemble formation of the Alkylhydroperoxide Reductase subunits. AhpC and AhpF from Escherichia coli
Structure, mechanism and ensemble formation of the Alkylhydroperoxide Reductase subunits AhpC and AhpF from Escherichia coli Phat Vinh Dip 1,#, Neelagandan Kamariah 2,#, Malathy Sony Subramanian Manimekalai
More informationProtein Structures: Experiments and Modeling. Patrice Koehl
Protein Structures: Experiments and Modeling Patrice Koehl Structural Bioinformatics: Proteins Proteins: Sources of Structure Information Proteins: Homology Modeling Proteins: Ab initio prediction Proteins:
More informationSupporting Information
Supporting Information Fera et al. 10.1073/pnas.1409954111 SI Methods Compliance. All work related to human subjects complied with protocols approved by the Duke University Health System Institutional
More informationfor Molecular Biology and Neuroscience and Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet
SUPPLEMENTARY INFORMATION TO Structural basis for enzymatic excision of N -methyladenine and N 3 -methylcytosine from DNA Ingar Leiros,5, Marivi P. Nabong 2,3,5, Kristin Grøsvik 3, Jeanette Ringvoll 2,
More informationStructural insights into WcbI, a novel polysaccharide-biosynthesis enzyme
Volume 1 (2014) Supporting information for article: Structural insights into WcbI, a novel polysaccharide-biosynthesis enzyme Mirella Vivoli, Emily Ayres, Edward Beaumont, Michail N. Isupov and Nicholas
More informationSecondary Structure. Bioch/BIMS 503 Lecture 2. Structure and Function of Proteins. Further Reading. Φ, Ψ angles alone determine protein structure
Bioch/BIMS 503 Lecture 2 Structure and Function of Proteins August 28, 2008 Robert Nakamoto rkn3c@virginia.edu 2-0279 Secondary Structure Φ Ψ angles determine protein structure Φ Ψ angles are restricted
More informationThe NRP peptidase ClbP as a target for the inhibition. of genotoxicity, cell proliferation and tumorogenesis. mediated by pks-harboring bacteria
1 1 1 1 1 1 1 1 0 1 0 The NRP peptidase ClbP as a target for the inhibition of genotoxicity, cell proliferation and tumorogenesis mediated by pks-harboring bacteria INTRODUCTION Nougayrède et al. recently
More informationFull-length GlpG sequence was generated by PCR from E. coli genomic DNA. (with two sequence variations, D51E/L52V, from the gene bank entry aac28166),
Supplementary Methods Protein expression and purification Full-length GlpG sequence was generated by PCR from E. coli genomic DNA (with two sequence variations, D51E/L52V, from the gene bank entry aac28166),
More informationGene regulation II Biochemistry 302. February 27, 2006
Gene regulation II Biochemistry 302 February 27, 2006 Molecular basis of inhibition of RNAP by Lac repressor 35 promoter site 10 promoter site CRP/DNA complex 60 Lewis, M. et al. (1996) Science 271:1247
More informationRNA protects a nucleoprotein complex against radiation damage
Supporting information Volume 72 (2016) Supporting information for article: RNA protects a nucleoprotein complex against radiation damage Charles S. Bury, John E. McGeehan, Alfred A. Antson, Ian Carmichael,
More informationFinal Chem 4511/6501 Spring 2011 May 5, 2011 b Name
Key 1) [10 points] In RNA, G commonly forms a wobble pair with U. a) Draw a G-U wobble base pair, include riboses and 5 phosphates. b) Label the major groove and the minor groove. c) Label the atoms of
More information