PDB Short entry for 1PUN HEADER HYDROLASE 25-JUN-03 1PUN TITLE SOLUTION STRUCTURE OF THE MUTT PYROPHOSPHOHYDROLASE COMPLEXED WITH TITLE 2 MG(2+) AND 8-OXO-DGMP, A TIGHTLY-BOUND PRODUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUTATOR MUTT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 7,8-DIHYDRO-8-OXOGUANINE-TRIPHOSPHATASE, 8-OXO-DGTPASE, DGTP COMPND 5 PYROPHOSPHOHYDROLASE; COMPND 6 EC: 3.6.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: MUTT,STRAIN: K12-I7023; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HMS174; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET MUTT, T7 PROMOTER KEYWDS MUTATOR PROTEIN, NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE, MUTT KEYWDS 2 PYROPHOSPHOHYDROLASE-METAL-PRODUCT COMPLEX, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.A.MASSIAH,V.SARASWAT,H.F.AZURMENDI,A.S.MILDVAN REVDAT 4 02-MAR-22 1PUN 1 REMARK LINK REVDAT 3 24-FEB-09 1PUN 1 VERSN REVDAT 2 27-JAN-04 1PUN 1 JRNL REVDAT 1 26-AUG-03 1PUN 0 JRNL AUTH M.A.MASSIAH,V.SARASWAT,H.F.AZURMENDI,A.S.MILDVAN JRNL TITL SOLUTION STRUCTURE AND NH EXCHANGE STUDIES OF THE MUTT JRNL TITL 2 PYROPHOSPHOHYDROLASE COMPLEXED WITH MG(2+) AND 8-OXO-DGMP, A JRNL TITL 3 TIGHTLY BOUND PRODUCT. JRNL REF BIOCHEMISTRY V. 42 10140 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12939141 JRNL DOI 10.1021/BI030105P REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.LIN,C.ABEYGUNAWARDANA,D.N.FRICK,M.J BESSMAN,A.S.MILDVAN REMARK 1 TITL SOLUTION STRUCTURE OF THE QUATERNARY COMPLEX REMARK 1 TITL 2 MUTT-M(2+)-AMPCPP-M(2+) COMPLEX AND MECHANISM OF ITS REMARK 1 TITL 3 PYROPHOSPHOHYDROLASE ACTION REMARK 1 REF BIOCHEMISTRY V. 36 1199 1997 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI962619C REMARK 1 REFERENCE 2 REMARK 1 AUTH D.N.FRICK,D.J.WEBER,C.ABEYGUNAWARDANA,A.G.GITTIS, REMARK 1 AUTH 2 M.J BESSMAN,A.S.MILDVAN REMARK 1 TITL NMR STUDIES OF THE CONFORMATIONS AND LOCATION OF NUCLEOTIDES REMARK 1 TITL 2 BOUND TO THE E.COLI MUTT ENZYME REMARK 1 REF BIOCHEMISTRY V. 34 5577 1995 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 3 REMARK 1 AUTH C.ABEYGUNAWARDANA,D.J.WEBER,A.G.GITTIS,D.N.FRICK,J.LIN, REMARK 1 AUTH 2 A.F.MILLER,M.J.BESSMAN,A.S.MILDVAN REMARK 1 TITL SOLUTION STRUCTURE OF THE MUTT ENZYME, A NUCLEOSIDE REMARK 1 TITL 2 TRIPHOSPHATE PYROPHOSPHOHYDROLASE REMARK 1 REF BIOCHEMISTRY V. 34 14997 1995 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.1, CNS 1.1 REMARK 3 AUTHORS : F. DELAGLIO (NMRPIPE), A. BRUNGER ET AL. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 1746 NOE REMARK 3 -DERIVED DISTANCE CONSTRAINTS, 186 DIHEDRAL ANGLE RESTRAINTS REMARK 3 DERIVED FROM TALOS, 82 DISTANCE RESTRAINTS FROM HYDROGEN BONDS REMARK 3 AND 53 N-H RESIDUAL DIPOLAR COUPLINGS. REMARK 4 REMARK 4 1PUN COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000019581. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295; 295 REMARK 210 PH : 7.5; 7.5 REMARK 210 IONIC STRENGTH : 21 MM NACL; 21 MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM MUTT, 1.3MM 8-OXO-DGMP, 15MM REMARK 210 MGCL2, 4MM D11-TRIS-HCL, PH 7.5, REMARK 210 21MM NACL, 0.34MM NAN3.; 1MM REMARK 210 MUTT, 1.3MM 8-OXO-DGMP, 15MM REMARK 210 MGCL2, 4MM D11-TRIS-HCL, PH 7.5, REMARK 210 21MM NACL, 0.34MM NAN3. REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 2D REMARK 210 NOESY; 2D TOCSY; 3D_13C- REMARK 210 SEPARATED_NOESY; 12C/13C- REMARK 210 FILTERED-NOESY-HSQC; 15N-1H IPAP- REMARK 210 HSQC; HNCA; NHCACB REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.1, TALOS 1999.019.15.47 REMARK 210 METHOD USED : SIMULATED ANNEALING TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: SAMPLE CONDITION 2 WAS USED TO MEASURE RESIDUAL DIPOLAR REMARK 210 COUPLINGS. 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 HOH A 5011 H1 HOH A 5014 0.96 REMARK 500 O HOH A 5011 H1 HOH A 5013 0.96 REMARK 500 O HOH A 5012 H2 HOH A 5014 0.96 REMARK 500 O HOH A 5012 H2 HOH A 5013 0.96 REMARK 500 O VAL A 50 H LEU A 54 1.54 REMARK 500 O ILE A 123 H LYS A 127 1.56 REMARK 500 O PHE A 65 O LEU A 86 2.14 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 ASN A 16 9.32 83.77 REMARK 500 1 PHE A 19 97.51 -61.51 REMARK 500 1 ARG A 23 -86.30 51.21 REMARK 500 1 ALA A 24 36.94 82.51 REMARK 500 1 ALA A 25 82.97 55.35 REMARK 500 1 ASP A 26 88.75 57.49 REMARK 500 1 ALA A 27 -165.54 -126.44 REMARK 500 1 ASN A 31 31.13 -95.11 REMARK 500 1 LEU A 33 57.62 -68.87 REMARK 500 1 PRO A 36 168.56 -47.88 REMARK 500 1 LYS A 39 19.70 105.16 REMARK 500 1 GLU A 41 -83.99 -44.19 REMARK 500 1 MET A 42 -91.93 44.86 REMARK 500 1 VAL A 58 -43.88 -134.26 REMARK 500 1 PHE A 65 -172.83 176.44 REMARK 500 1 SER A 66 154.78 76.94 REMARK 500 1 PRO A 76 80.35 -34.88 REMARK 500 1 ASP A 77 -47.81 87.52 REMARK 500 1 TRP A 95 -62.55 -132.90 REMARK 500 1 LYS A 97 41.77 173.45 REMARK 500 2 ASN A 16 9.98 81.99 REMARK 500 2 PHE A 19 94.42 -65.72 REMARK 500 2 ARG A 23 16.31 56.13 REMARK 500 2 ALA A 24 -163.36 43.28 REMARK 500 2 ALA A 27 -159.51 67.33 REMARK 500 2 HIS A 28 173.14 68.87 REMARK 500 2 ASN A 31 31.24 -93.44 REMARK 500 2 LEU A 33 89.53 -46.70 REMARK 500 2 LYS A 39 19.99 98.82 REMARK 500 2 GLU A 41 -82.35 -44.01 REMARK 500 2 MET A 42 -87.72 42.68 REMARK 500 2 VAL A 58 -44.46 -132.97 REMARK 500 2 PHE A 65 -167.41 172.49 REMARK 500 2 SER A 66 158.08 72.58 REMARK 500 2 PRO A 76 86.25 -49.87 REMARK 500 2 ASP A 77 28.78 92.51 REMARK 500 2 TRP A 95 -63.51 -134.22 REMARK 500 2 LYS A 97 35.12 174.33 REMARK 500 2 TRP A 104 107.11 -58.95 REMARK 500 3 ASN A 16 15.88 86.17 REMARK 500 3 PHE A 19 95.77 -62.25 REMARK 500 3 ARG A 23 30.94 39.92 REMARK 500 3 ALA A 24 -166.87 49.98 REMARK 500 3 ASP A 26 -54.30 -152.74 REMARK 500 3 HIS A 28 77.72 -179.35 REMARK 500 3 MET A 29 108.34 64.11 REMARK 500 3 ASN A 31 31.10 -95.62 REMARK 500 3 LEU A 33 62.55 -65.53 REMARK 500 3 LYS A 39 -8.11 116.55 REMARK 500 3 ILE A 40 -73.78 -40.97 REMARK 500 REMARK 500 THIS ENTRY HAS 380 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1 HOH A 5013 REMARK 610 1 HOH A 5014 REMARK 610 2 HOH A 5025 REMARK 610 2 HOH A 5026 REMARK 610 3 HOH A 5037 REMARK 610 3 HOH A 5038 REMARK 610 4 HOH A 5049 REMARK 610 4 HOH A 5050 REMARK 610 5 HOH A 5061 REMARK 610 5 HOH A 5062 REMARK 610 6 HOH A 5073 REMARK 610 6 HOH A 5074 REMARK 610 7 HOH A 5085 REMARK 610 7 HOH A 5086 REMARK 610 8 HOH A 5097 REMARK 610 8 HOH A 5098 REMARK 610 9 HOH A 5109 REMARK 610 9 HOH A 5110 REMARK 610 10 HOH A 5121 REMARK 610 10 HOH A 5122 REMARK 610 11 HOH A 5133 REMARK 610 11 HOH A 5134 REMARK 610 12 HOH A 5145 REMARK 610 12 HOH A 5146 REMARK 610 13 HOH A 5157 REMARK 610 13 HOH A 5158 REMARK 610 14 HOH A 5169 REMARK 610 14 HOH A 5170 REMARK 610 15 HOH A 5181 REMARK 610 15 HOH A 5182 REMARK 610 16 HOH A 5193 REMARK 610 16 HOH A 5194 REMARK 610 17 HOH A 5205 REMARK 610 17 HOH A 5206 REMARK 610 18 HOH A 5217 REMARK 610 18 HOH A 5218 REMARK 610 19 HOH A 5229 REMARK 610 19 HOH A 5230 REMARK 610 20 HOH A 5241 REMARK 610 20 HOH A 5242 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 MG A 130 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 38 O REMARK 620 2 GLU A 53 OE2 97.1 REMARK 620 3 GLU A 53 OE1 86.4 11.0 REMARK 620 4 GLU A 56 OE1 164.0 70.7 80.9 REMARK 620 5 GLU A 57 OE2 82.0 109.1 105.5 92.0 REMARK 620 6 HOH A5011 O 100.4 79.0 83.0 87.7 171.3 REMARK 620 7 HOH A5012 O 71.1 162.2 154.8 123.1 83.0 89.9 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 130 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 8OG A 131 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PPX RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE SAME COMPLEX WITHOUT RESIDUAL DIPOLAR REMARK 900 COUPLINGS REMARK 900 RELATED ID: 1MUT RELATED DB: PDB REMARK 900 THE FREE SOLUTION STRUCTURE REMARK 900 RELATED ID: 1TUM RELATED DB: PDB REMARK 900 COMPLEXED WITH AMPCPP-MG. REMARK 900 RELATED ID: 1PUQ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE MUTT PYROPHOSPHOHYDROLASE COMPLEXED WITH REMARK 900 MG(2+) AND 8-OXO-DGMP, A TIGHTLY-BOUND PRODUCT REMARK 900 RELATED ID: 1PUS RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE MUTT PYROPHOSPHOHYDROLASE COMPLEXED WITH REMARK 900 MG(2+) AND 8-OXO-DGMP, A TIGHTLY-BOUND PRODUCT DBREF 1PUN A 1 129 UNP P08337 MUTT_ECOLI 1 129 SEQRES 1 A 129 MET LYS LYS LEU GLN ILE ALA VAL GLY ILE ILE ARG ASN SEQRES 2 A 129 GLU ASN ASN GLU ILE PHE ILE THR ARG ARG ALA ALA ASP SEQRES 3 A 129 ALA HIS MET ALA ASN LYS LEU GLU PHE PRO GLY GLY LYS SEQRES 4 A 129 ILE GLU MET GLY GLU THR PRO GLU GLN ALA VAL VAL ARG SEQRES 5 A 129 GLU LEU GLN GLU GLU VAL GLY ILE THR PRO GLN HIS PHE SEQRES 6 A 129 SER LEU PHE GLU LYS LEU GLU TYR GLU PHE PRO ASP ARG SEQRES 7 A 129 HIS ILE THR LEU TRP PHE TRP LEU VAL GLU ARG TRP GLU SEQRES 8 A 129 GLY GLU PRO TRP GLY LYS GLU GLY GLN PRO GLY GLU TRP SEQRES 9 A 129 MET SER LEU VAL GLY LEU ASN ALA ASP ASP PHE PRO PRO SEQRES 10 A 129 ALA ASN GLU PRO VAL ILE ALA LYS LEU LYS ARG LEU HET MG A 130 1 HET 8OG A 131 36 HETNAM MG MAGNESIUM ION HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 8OG C10 H14 N5 O8 P FORMUL 4 HOH *4(H2 O) HELIX 1 1 GLU A 47 GLU A 57 1 11 HELIX 2 2 SER A 106 LEU A 110 5 5 HELIX 3 3 PRO A 116 ALA A 118 5 3 HELIX 4 4 ASN A 119 ARG A 128 1 10 SHEET 1 A 3 LYS A 2 ILE A 10 0 SHEET 2 A 3 ARG A 78 LEU A 86 1 O TRP A 83 N VAL A 8 SHEET 3 A 3 GLU A 69 GLU A 74 -1 N GLU A 69 O PHE A 84 SHEET 1 B 2 ILE A 18 ILE A 20 0 SHEET 2 B 2 GLU A 103 MET A 105 -1 O MET A 105 N ILE A 18 LINK O GLY A 38 MG MG A 130 1555 1555 2.35 LINK OE2 GLU A 53 MG MG A 130 1555 1555 4.51 LINK OE1 GLU A 53 MG MG A 130 1555 1555 2.40 LINK OE1 GLU A 56 MG MG A 130 1555 1555 2.22 LINK OE2 GLU A 57 MG MG A 130 1555 1555 2.40 LINK MG MG A 130 O HOH A5011 1555 1555 2.11 LINK MG MG A 130 O HOH A5012 1555 1555 2.11 SITE 1 AC1 7 GLY A 38 LYS A 39 GLU A 53 GLU A 56 SITE 2 AC1 7 GLU A 57 HOH A5011 HOH A5012 SITE 1 AC2 3 LEU A 4 ILE A 6 GLU A 41 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