Figure 2. Amino acid sequence alignment of L-carbamoylases. A BLAST search was conducted with BsLcar sequence, using the UNIREF100 sequence cluster
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1 Figure 1. A) Simulated MIT MAP at 1.2 σ contours (blue), generated by shaking the coordinates using PDBSET from the CCP4 program suite [1], removing cacodylate molecule from the model, and refining 5 cycles with REFMAC5 [2]. FoFc map at 3.5 σ contours is represented in green. B) The same maps showing the position of several residues in the proximity of the blob corresponding to the cacodylate molecule. Both figures were generated with CCP4MG program [3]. C) Deposited structure (PDB ID. 35F) showing roughly the same orientation as in A) and B). 2FoFc and FoFc maps are at 1.4 σ and 3.5 σ contours, respectively) A) B) C)
2 Figure 2. Amino acid sequence alignment of Lcarbamoylases. A BLAST search was conducted with BsLcar sequence, using the UIREF100 sequence cluster [4] to remove sequence redundancy and to reduce the number of sequences. Lcarbamoylases with proven activity were included for comparison. AMAB2_GESE (GenBank ID Q53389 [5]), AMAB1_GESE (GenBank ID P37113 [5]), GeokaLcar (GenBank ID Q8GQG5 [6]), AaurhyuC (GenBank ID Q9F464 [7]), YUC_Pse (GenBank ID Q01264 [8]) and SmeLcar (GenBank ID Q92MZ4 [9,10]). ClustalW XXL was used for sequence alignment. ESPript [11] was used to generate the images and to show the secondary structure of BsLcar. The consensus sequence appears below. The residues mutated in this work are highlighted in a box; residues forming the conserved bimetallic center appear as asterisks and substrate binding and hydrolysis residues as crosses.
3 Figure 2. Sequence alignment of Lcarbamoylases. (Cont.) * * *
4 Figure 2. Sequence alignment of Lcarbamoylases. (Cont.) *
5 Figure 2. Sequence alignment of Lcarbamoylases. (Cont.) *
6 Figure 3. Superposed CD spectra of wildtype and mutated BsLcar species (5µM) in sodium phosphate buffer 100 mm p 7.5. T [V] CD [mdeg] Wavelength [nm]
7 Figure 4. Schematic reaction mechanism of BsLcar toward different Lsubstitutedαamino acids, based on previous proposed mechanisms [12,13]. The second metallic atom () can be present or not, according to the results shown for BsLcar (see Results and discussionsection). X= 2, Lcarbamoylαamino acid; X= C 3, Lacetylαamino acid; X=, Lformylαamino acid; In the product release, ( 3 C 2 ), acetate or formiate are produced depending on the substrate used (carbamoyl, acetyl or formylderivative). Lsubstitutedαamino acid Substrate binding X 3 2 is225 is380 is189 is R is225 is380 Domain motion Water activation is189 is79 3 X 2 R is225 is380 is189 is79 Domain motion Products release 3 2 X 2 R is225 is380 is189 is79 3 X 2 R is225 is380 is189 is79
8 Supplementary references. 1. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A, Mcicholas SJ, Murshudov G, Pannu S, Potterton EA, Powell R, Read RJ, Vagin A, Wilson KS verview of the CCP4 suite and current developments. Acta Crystallogr. D: 67: Murshudov G, Skubák P, Lebedev AA, Pannu S, Steiner RA, icholls RA, Winn MD, Long F, Vagin AA REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D 67: Mcicholas S, Potterton E, Wilson KS, oble MEM Presenting your structures: the CCP4mg moleculargraphics software. Acta Crystallogr. D 67: Suzek BE, uang, McGarvey P, Mazumder R, Wu C UniRef:comprehensive and nonredundant UniProt reference clusters. Bioinformatics 23: Batisse, Weigel P, Lecocq M, Sakanyan V Two amino acid amidohydrolase genes encoding Lstereospecific carbamoylase and aminoacylase are organized in a common operon in Bacillus stearothermophilus. Appl. Envir. Microbiol. 63: u Y, su W, Chien R Characterization and phylogenetic analysis of a thermostable carbamoyllamino acid amidohydrolase from Bacillus kaustophilus CCRC Arch. Microbiol. 179: Wilms B, Wiese A, Syldatk C, Mattes R, Altenbuchner J, Pietzsch M Cloning, nucleotide sequence and expression of a new Lcarbamoylase gene from Arthrobacter aurescens DSM 3747 in E. coli. J. Biotechnol. 68: Ishikawa T, Watabe K, Mukohara Y, akamura carbamyllamino acid amidohydrolase of Pseudomonas sp. strain S671: purification and some properties of the enzyme expressed in Escherichia coli. Biosci. Biotechnol. Biochem. 60:
9 9. MartínezRodríguez S, ClementeJiménez JM, RodríguezVico F, Las eras Vázquez FJ Molecular cloning and biochemical characterization of Lcarbamoylase from Sinorhizobium meliloti CECT4114. J. Mol. Microbiol. Biotechnol. 9: MartínezRodríguez S, AndújarSánchez M, Clemente Jiménez JM, JaraPérez V, RodríguezVico F, Las erasvázquez FJ Thermodynamic and mutational studies of Lcarbamoylase from Sinorhizobium meliloti CECT 4114 catalytic centre. Biochimie 88: Gouet P, Courcelle E, Stuart DI, Metoz F ESPript: multiple sequence alignments in PostScript. Bioinformatics 15: Lundgren S, Gojkovic Z, Piškur J, Dobritzsch D Yeast βalanine synthase shares a structural scaffold and origin with dizincdependent exopeptidases. J. Biol. Chem. 278: olz RC, Bzymek KP, Swierczek SI Cocatalytic metallopeptidases as pharmaceutical targets. Curr. pin. Chem. Biol. 7:
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