for Molecular Biology and Neuroscience and Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet

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1 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, Gyri T. Haugland 4, Lene Uldal 2, Karen Reite 2, Inger K. Olsbu 3, Ingeborg Knævelsrud 3,4, Elin Moe, Ole A. Andersen, Nils-Kåre Birkeland 4, Peter Ruoff 3, Arne Klungland 2 and Svein Bjelland 3, * The Norwegian Structural Biology Centre, University of Tromsø, N-937 Tromsø, Norway. 2 Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet HF, University of Oslo, N-27 Oslo, Norway. 3 Faculty of Science and Technology, Department of Mathematics and Natural Sciences, University of Stavanger, N-436 Stavanger, Norway. 4 Department of Biology, University of Bergen, PO Box 78, N-52 Bergen, Norway. 5 These authors contributed equally to this work. *Corresponding author. Faculty of Science and Technology, Department of Mathematics and Natural Sciences, University of Stavanger, N-436 Stavanger, Norway. Tel.: ; Fax: ; svein.bjelland@uis.no

2 Derivation of kinetic equations for AfAlkA The reaction catalyzed by AfAlkA (E) can be summarized as DNA P (R) where P represents products (i.e. DNA and free base lesion). Reaction R is a first-order process with reaction rate v=d[p]/dt = k [DNA] () Equation is readily solved and the increase of product concentration [P] as a function of time t is given by the equation [P] = [DNA] ( e k t ) (2) where [DNA] denotes the al (initial) DNA substrate concentration and k is the (first-order) rate constant. The experimental results can be interpreted by considering a non-specific glycosylase binding or adsorption to DNA and looking specifically at the site where catalysis (excision) is taking place, i.e., the specific position where m A, εa or m 3 C are inserted (Figure A). If DNA i is the location i on the DNA where catalysis occurs (when E binds to this site) we can write k k E + DNA E DNA 2 i E + DNA + free base lesion (R2) k i - Considering this process, we can write the following mass balance at DNA i : [DNA] = [DNA i ] + [E DNA i ] (3) where [DNA] is the al DNA concentration, E DNA i denotes any DNA molecule where E occupies the catalytic site i, and DNA i is any DNA molecule where E has not bound to the excision site i. Calculating d[e DNA i ]/dt and assuming that E DNA i is in a steady state (leading to d[e DNA i ]/dt = ), it results in d[e DNA i ]/dt = k [E][DNA i ] (k + k 2 )[E DNA i ] = (4) By inserting [DNA i ] from Equation 3 into Equation 4, the steady state value of [E DNA i ], [E DNA i ] ss, can be expressed as 2

3 with [E][DNA] [E DNA i ] ss = K + [E] k D + K D = k k 2 (5) Because the concentration of E is in excess of the DNA template (single-turnover conditions; [E] >> [DNA] ), [E] in Equation 5 can be replaced by [E] : [E DNA i ] ss [E] = (6) K + [E] D [DNA] Since the reaction rate is expressed by ν = k 2 [E DNA i ] ss, ν can be written as [E] [DNA] ν = k2 (7) K D + [E] showing that the rate constant k of Equation is specified by the following relationship: k E] k = 2[ K + [ E] D (8) An analogous expression to Equation 7 can be derived by assuming a rapid equilibrium between E, DNA i and E DNA i. In this case K D is represented by k /k. In the case reaction R2 is irreversible (k = ), K D = k 2 /k. Due to these situations it is difficult to make a precise interpretation about the physical nature of K D based on k 2 and K D values alone. The observation that for m A, k 2 is decreased while K D is increased for most of the mutant proteins (Table I), may suggest that the binding between the DNA and the enzyme has become less effective with a somewhat slower turnover. For εa, both k 2 and K D are decreased for the mutant compared to the wild-type proteins (Table I). This may indicate the presence of a steady state with still a relatively strong binding between DNA and the enzyme, but with a less effective turnover. 3

4 Supplementary Table I Data collection, structure solution and refinement statistics Dataset Peak Native Data collection statistics Beamline ID4-4 BL4. Wavelength (Å).9.99 Resolution range (Å) 2..8(.9.8) 5.-.9(.95-.9) R sym (%) 8.4(49.9) 6.7(43.4) Multiplicity 8.(7.6) 2.9(2.9) Mean I/σI 8.(3.5).4(2.5) Completeness (%) 98.7(97.9) 99.9(.) Anom. completeness (%) 98.5(97.5) - Space group P2 P2 Unit cell parameters: Phasing statistics a(å) b(å) c(å) β( ) No. Heavy atoms/a.s.u. 2 Hg - R cullis Phasing power FOM SHARP.43 - FOM DM Refinement statistics No. Atoms 5493/49/495/4/4/4/4 5425/4826/57//4/4/ B-factors 2/9/29/33 /27 /8/33 2/9/3//34/2/ R free (%) R work (%) Geometrical deviation Bonds (Å).5.5 Angles ( ) ESU (Å).78. : Two additional Mercury atoms were identified at the refinement stage through phased anomalous fourier maps, but were not used at the preceding phasing stage. : Figure-ofmerit (FOM) from SHARP-phasing for acentric data to 2.5 Å. : FOM from DM after extending phases to.8 Å. : Total/Protein/Water/Mercury/Glycerol molecules/sodium/mes molecules. : Modeled with reduced occupancy. : Estimated overall coordinate error from REFMAC5 based on maximum likelihood. 4

5 Supplementary Table II Structural alignment of domains of AfAlkA and EcAlkA EcAlkA (#aligned/al) rmsd (Å) Domain AfAlkA (84/).55 N-term (33/48).4 Central (4/3).38 C-term (59/289).58 All residues The table illustrates structural conservation between individual domains of AfAlkA and EcAlkA, where the numbers in parenthesis are number of residues aligned out of the al number of residues in that domain and the last number lists the root mean square deviation (rmsd) between the aligned residues in AfAlkA and EcAlkA. 5

6 Supplementary Figure 6

7 Legend to Supplementary Figure Exposure of EcAlkA to m A- and m 3 C- containing DNA. Assay for cleavage of 5 [ 32 P]labeled 49-nt DNA into repair product (23 and 25 nt) is described in FigureA,B. EcAlkA was incubated with DNA ( fmol) in 5 mm Hepes [4-(2-hydroxyethyl)--piperazineethanesulfonic acid]-koh, ph 7.5,.3 mm EDTA,.5 mm 2-mercaptoethanol at 37 C for 3 min (The same result was obtained when incubation was carried out at 37 C under exactly the same conditions as employed for AfAlkA). 7

8 Supplementary Figure 2 8

9 Legend to Supplementary Figure 2 Stereo representation showing the superpositioning of the Cα-traces of AfAlkA (red) and Ec AlkA (black). Af AlkA residue numbers are labeled. 9

10 Supplementary Figure 3

11 Legend to Supplementary Figure 3 Sliced view of the molecular surface of AfAlkA enabling visualization of the water-accessible channel extending from the base of the substrate-binding pocket into the core of the protein. The modeled εa moiety is shown with orange carbon atoms, while protein carbon atoms are shown in dark green. Other atoms are shown in atom colors (oxygen, red; nitrogen blue; sulfur, yellow). The cavity contains a al of one glycerol and 3 water molecules. The electrostatic surface potential is calculated as for Figure 4.

12 Supplementary Figure 4 2

13 Legend to Supplementary Figure 4 SDS PAGE (2 %) of purified AfAlkA mutant and wild type proteins stained with Coomassie Blue. Samples (2 μg; μl) and protein markers ( μl; BenchMark Pre-Stained Protein Ladder, Cat. No. 748-, Invitrogen) were loaded onto the gel (Bio-Rad, Ready Gel Tris HCl Gels, 2 % Resolving Gel, Cat. # 6-56) and run for 2 h at 2 V. 3

14 Supplementary Figure 5.4 m A (Gln28Ala).6 m A (Phe33Ala) [E]= nm [E]=6 nm [E]=25 nm.4 [E]=5 nm.2 [E]= nm m A (Phe282Ala) [E]= nm [E]=6 nm [E]=25 nm [E]= nm [E]= nm [E]=6 nm [E]=25 nm [E]= nm m A (Phe33Ala/Phe282Ala).6.4 [E]= nm m A (Arg286Ala) [E]= nm [E]=6 nm [E]=25 nm [E]=5 nm [E]= nm 4

15 Legend to Supplementary Figure 5 Single-turnover kinetics for excision of m A, where nm of substrate was incubated with different concentrations of AfAlkA at 7 C for increasing time periods. Each value represents the average of three independent measurements. 5

16 Supplementary Figure 6 ε A (Gln28Ala) 8 7 [E]=25 nm [E]=5 nm 3 2 [E]= nm [E]=5 nm ε A (Phe33Ala) 6 [E]=25 nm [E]=5 nm [E]= nm [E]=5 nm 6 ε A (Phe282Ala).2 ε A (Phe33Ala/Phe282Ala) 5 [E]=25 nm 4 [E]=5 nm 3 2 [E]= nm [E]=5 nm [E]=25 nm.8.6 [E]=5 nm.4.2 [E]= nm 5 ε A (Arg286Ala) [E]=25 nm [E]= nm [E]=5 nm [E]=5 nm 6

17 Legend to Supplementary Figure 6 Single-turnover kinetics for excision of εa, where nm of substrate was incubated with different concentrations of AfAlkA at 7 C for increasing time periods. Each value represents the average of 2 3 independent measurements. 7