HEADER HYDROLASE 02-MAY-03 1P7M TITLE SOLUTION STRUCTURE AND BASE PERTURBATION STUDIES REVEAL A NOVEL MODE TITLE 2 OF ALKYLATED BASE RECOGNITION BY 3-METHYLADENINE DNA GLYCOSYLASE I COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-3-METHYLADENINE GLYCOSYLASE I; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.20; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: TAG OR B3549; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: STRAIN B; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS 3-METHYLADENINE TAG COMPLEX NMR, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR C.CAO,K.KWON,Y.L.JIANG,A.C.DROHAT,J.T.STIVERS REVDAT 3 23-FEB-22 1P7M 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1P7M 1 VERSN REVDAT 1 25-NOV-03 1P7M 0 JRNL AUTH C.CAO,K.KWON,Y.L.JIANG,A.C.DROHAT,J.T.STIVERS JRNL TITL SOLUTION STRUCTURE AND BASE PERTURBATION STUDIES REVEAL A JRNL TITL 2 NOVEL MODE OF ALKYLATED BASE RECOGNITION BY 3-METHYLADENINE JRNL TITL 3 DNA GLYCOSYLASE I JRNL REF J.BIOL.CHEM. V. 278 48012 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 13129925 JRNL DOI 10.1074/JBC.M307500200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, X-PLOR NIH-2.0.2 REMARK 3 AUTHORS : BRUNGER, A.T., ADAMS, P.D., CLORE, G.M., DELANO, REMARK 3 W.L., GROS, P., GROSSE-KUNSTLEVE, R.W., JIANG, J.- REMARK 3 S., KUSZEWSKI, J., NILGES, M., PANNU, N.S., READ, REMARK 3 R.J., RICE, L.M., SIMONSON, T., WARREN, G.L. (CNS), REMARK 3 CLORE, G.M., KUSZEWSKI, J. (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 2494 RESTRAINTS, 2140 ARE REMARK 3 NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 222 DIHEDRAL ANGLE RESTRAINTS, 132 H-BOND CONSTRAINTS REMARK 4 REMARK 4 1P7M COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019108. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.6 REMARK 210 IONIC STRENGTH : 10MM PHOSPHATE BUFFER REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5-1MM 13C, 15N, 75% 2H REMARK 210 LABELED3-METHYLADENINE DNA REMARK 210 GLYCOSYLASE I, 100MM NACL, 3MM REMARK 210 DTT, 0.34MM NAN3, 10MM PHOSPHATE REMARK 210 BUFFER, PH6.6 ~8, FOLD ( OR 13C8 REMARK 210 LABELED) 3-METHYLADENINE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D NOESY; 13C- REMARK 210 EDITED HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX; UNITYPLUS; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.93, NMRPIPE NIH REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND ENERGY, REMARK 210 STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 8 REMARK 210 REMARK 210 REMARK: 1H-13C HMQC REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O TYR A 16 HD21 ASN A 19 1.46 REMARK 500 O ALA A 69 HH21 ARG A 100 1.48 REMARK 500 O LYS A 52 H TYR A 56 1.54 REMARK 500 O CYS A 179 H CYS A 181 1.56 REMARK 500 O TRP A 117 H HIS A 122 1.57 REMARK 500 O LEU A 37 HE21 GLN A 41 1.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ARG A 3 -92.29 -87.30 REMARK 500 1 GLU A 20 75.19 173.11 REMARK 500 1 GLN A 41 1.96 -69.07 REMARK 500 1 HIS A 61 17.08 -56.97 REMARK 500 1 PHE A 63 29.09 38.32 REMARK 500 1 ALA A 83 -11.50 70.20 REMARK 500 1 ILE A 85 -172.63 -52.18 REMARK 500 1 ILE A 86 92.06 -61.68 REMARK 500 1 HIS A 88 73.77 -178.36 REMARK 500 1 HIS A 122 26.10 48.78 REMARK 500 1 ASP A 174 42.56 -161.58 REMARK 500 1 VAL A 176 11.07 175.51 REMARK 500 1 VAL A 177 117.97 58.37 REMARK 500 1 CYS A 179 79.48 -67.84 REMARK 500 1 CYS A 180 -48.30 68.93 REMARK 500 1 CYS A 181 71.71 -170.27 REMARK 500 1 ASN A 185 -72.83 -87.69 REMARK 500 2 GLN A 9 -108.69 -95.78 REMARK 500 2 GLU A 20 48.11 -174.42 REMARK 500 2 GLN A 41 6.98 -61.26 REMARK 500 2 HIS A 61 -56.18 63.79 REMARK 500 2 PHE A 63 27.39 38.73 REMARK 500 2 ALA A 83 -19.81 67.56 REMARK 500 2 ILE A 85 -94.09 -29.28 REMARK 500 2 ILE A 86 -37.88 -170.58 REMARK 500 2 PHE A 156 61.51 61.71 REMARK 500 2 ASP A 174 -34.83 156.06 REMARK 500 2 HIS A 175 -82.49 55.88 REMARK 500 2 VAL A 177 27.60 34.80 REMARK 500 2 LYS A 186 73.33 44.65 REMARK 500 3 ARG A 3 -103.20 -57.26 REMARK 500 3 ASN A 19 -72.17 -91.33 REMARK 500 3 GLU A 20 81.67 -154.57 REMARK 500 3 GLN A 41 -6.54 -48.27 REMARK 500 3 PHE A 63 -88.76 -109.91 REMARK 500 3 ASP A 64 -73.09 87.62 REMARK 500 3 PRO A 65 -106.98 -97.19 REMARK 500 3 ALA A 83 -15.59 61.84 REMARK 500 3 ILE A 85 -178.38 -47.86 REMARK 500 3 ILE A 86 -105.26 -55.63 REMARK 500 3 HIS A 122 24.32 41.92 REMARK 500 3 ASP A 174 81.17 90.26 REMARK 500 3 VAL A 176 29.09 -158.10 REMARK 500 3 VAL A 177 2.50 53.01 REMARK 500 3 CYS A 181 24.08 -73.03 REMARK 500 4 GLN A 9 -159.38 -90.64 REMARK 500 4 ASP A 10 155.60 -44.75 REMARK 500 4 GLU A 20 24.73 -155.97 REMARK 500 4 VAL A 23 -35.61 -157.89 REMARK 500 4 VAL A 80 -17.37 -48.28 REMARK 500 REMARK 500 THIS ENTRY HAS 381 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 188 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 4 SG REMARK 620 2 HIS A 17 NE2 106.8 REMARK 620 3 HIS A 175 ND1 112.9 106.2 REMARK 620 4 CYS A 179 SG 109.0 111.4 110.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 188 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADK A 189 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LMZ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF 3-METHYLADENINE DNA GLYCOSYLASE I (TAG) REMARK 900 RELATED ID: 1NKU RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF ZINC-BINDING PROTEIN 3-METHYLADENINE DNA REMARK 900 GLYCOSYLASE I (TAG) DBREF 1P7M A 1 187 UNP P05100 3MG1_ECOLI 1 187 SEQADV 1P7M MET A 126 UNP P05100 VAL 126 CONFLICT SEQADV 1P7M TYR A 182 UNP P05100 HIS 182 CONFLICT SEQRES 1 A 187 MET GLU ARG CYS GLY TRP VAL SER GLN ASP PRO LEU TYR SEQRES 2 A 187 ILE ALA TYR HIS ASP ASN GLU TRP GLY VAL PRO GLU THR SEQRES 3 A 187 ASP SER LYS LYS LEU PHE GLU MET ILE CYS LEU GLU GLY SEQRES 4 A 187 GLN GLN ALA GLY LEU SER TRP ILE THR VAL LEU LYS LYS SEQRES 5 A 187 ARG GLU ASN TYR ARG ALA CYS PHE HIS GLN PHE ASP PRO SEQRES 6 A 187 VAL LYS VAL ALA ALA MET GLN GLU GLU ASP VAL GLU ARG SEQRES 7 A 187 LEU VAL GLN ASP ALA GLY ILE ILE ARG HIS ARG GLY LYS SEQRES 8 A 187 ILE GLN ALA ILE ILE GLY ASN ALA ARG ALA TYR LEU GLN SEQRES 9 A 187 MET GLU GLN ASN GLY GLU PRO PHE ALA ASP PHE VAL TRP SEQRES 10 A 187 SER PHE VAL ASN HIS GLN PRO GLN MET THR GLN ALA THR SEQRES 11 A 187 THR LEU SER GLU ILE PRO THR SER THR PRO ALA SER ASP SEQRES 12 A 187 ALA LEU SER LYS ALA LEU LYS LYS ARG GLY PHE LYS PHE SEQRES 13 A 187 VAL GLY THR THR ILE CYS TYR SER PHE MET GLN ALA CYS SEQRES 14 A 187 GLY LEU VAL ASN ASP HIS VAL VAL GLY CYS CYS CYS TYR SEQRES 15 A 187 PRO GLY ASN LYS PRO HET ZN A 188 1 HET ADK A 189 18 HETNAM ZN ZINC ION HETNAM ADK 3-METHYL-3H-PURIN-6-YLAMINE HETSYN ADK 3-METHYLADENINE FORMUL 2 ZN ZN 2+ FORMUL 3 ADK C6 H7 N5 HELIX 1 1 ASP A 10 TRP A 21 1 12 HELIX 2 2 ASP A 27 GLN A 41 1 15 HELIX 3 3 SER A 45 PHE A 60 1 16 HELIX 4 4 ASP A 64 MET A 71 1 8 HELIX 5 5 GLN A 72 VAL A 80 1 9 HELIX 6 6 HIS A 88 ASN A 108 1 21 HELIX 7 7 PRO A 111 VAL A 120 1 10 HELIX 8 8 THR A 131 ILE A 135 5 5 HELIX 9 9 THR A 139 ARG A 152 1 14 HELIX 10 10 GLY A 158 GLY A 170 1 13 SHEET 1 A 2 GLN A 125 MET A 126 0 SHEET 2 A 2 VAL A 172 ASN A 173 1 O ASN A 173 N GLN A 125 LINK SG CYS A 4 ZN ZN A 188 1555 1555 2.31 LINK NE2 HIS A 17 ZN ZN A 188 1555 1555 2.00 LINK ND1 HIS A 175 ZN ZN A 188 1555 1555 2.01 LINK SG CYS A 179 ZN ZN A 188 1555 1555 2.31 SITE 1 AC1 4 CYS A 4 HIS A 17 HIS A 175 CYS A 179 SITE 1 AC2 7 TRP A 6 TYR A 13 TYR A 16 TRP A 21 SITE 2 AC2 7 GLU A 38 TRP A 46 SER A 164 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20 MODEL 21 MODEL 22 MODEL 23 MODEL 24 MODEL 25