HEADER HYDROLASE 25-OCT-01 1IRY TITLE SOLUTION STRUCTURE OF THE HMTH1, A NUCLEOTIDE POOL SANITIZATION ENZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: HMTH1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE; COMPND 5 EC: 3.1.6.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HMTH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS NUDIX MOTIF(G37-L59), HYDROLASE EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR M.MISHIMA,N.ITOH,Y.SAKAI,H.KAMIYA,Y.NAKABEPPU,M.SHIRAKAWA REVDAT 5 27-DEC-23 1IRY 1 REMARK REVDAT 4 23-FEB-22 1IRY 1 REMARK REVDAT 3 24-FEB-09 1IRY 1 VERSN REVDAT 2 08-MAR-05 1IRY 1 AUTHOR JRNL REVDAT 1 23-DEC-03 1IRY 0 JRNL AUTH M.MISHIMA,Y.SAKAI,N.ITOH,H.KAMIYA,M.FURUICHI,M.TAKAHASHI, JRNL AUTH 2 Y.YAMAGATA,S.IWAI,Y.NAKABEPPU,M.SHIRAKAWA JRNL TITL STRUCTURE OF HUMAN MTH1, A NUDIX FAMILY HYDROLASE THAT JRNL TITL 2 SELECTIVELY DEGRADES OXIDIZED PURINE NUCLEOSIDE JRNL TITL 3 TRIPHOSPHATES JRNL REF J.BIOL.CHEM. V. 279 33806 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15133035 JRNL DOI 10.1074/JBC.M402393200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, CNS 1.0 REMARK 3 AUTHORS : GUENTERT, P. (DYANA), BRUNGER, A.T. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 2312 RESTRAINTS, 2043 ARE REMARK 3 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 177 DIHEDRAL ANGLE RESTRAINTS,92 DISTANCE REMARK 3 RESTRAINTS REMARK 3 FROM HYDROGEN BONDS DETECTED THROUGH 3HJNC. REMARK 4 REMARK 4 1IRY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1000005219. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : 70 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.7MM HMTH1 U-15N,13C; 50MM K REMARK 210 -PHOSPHATE BUFFER, 20MM KCL, REMARK 210 0.1MM EDTA AND 1MM DTT; 95% H2O, REMARK 210 5% D2O; 1.7MM HMTH1 U-15N,13C; REMARK 210 50MM K-PHOSPHATE BUFFER, 20MM REMARK 210 KCL, 0.1MM EDTA AND 1MM DTT; REMARK 210 99.8% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; REMARK 210 4D_13C/15N-SEPARATED_NOESY; HNHA; REMARK 210 4D_13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 1.8, XWINNMR 2.6, REMARK 210 NMRPIPP 4.2.4 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: STEREOSPECIFIC ASSIGNMENTS OF THE METHYL GROUPS OF THE REMARK 210 LEUCINE AND VALINE RESIDUES WERE ACHIEVED WITH 15% FRACTIONALLY REMARK 210 13C-LABELED HMTH1 DISSOLVED IN 99.8% D2O. 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 THR A 94 H VAL A 96 1.58 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 ALA A 3 -176.02 -170.20 REMARK 500 1 SER A 4 91.44 59.72 REMARK 500 1 ARG A 5 96.18 -67.41 REMARK 500 1 PRO A 15 33.34 -65.17 REMARK 500 1 GLN A 16 -42.68 -160.45 REMARK 500 1 ARG A 25 119.76 -169.80 REMARK 500 1 PHE A 27 74.88 -100.24 REMARK 500 1 ALA A 29 93.22 -55.70 REMARK 500 1 GLN A 40 171.76 -46.57 REMARK 500 1 GLU A 41 65.86 -68.05 REMARK 500 1 ALA A 63 101.10 179.54 REMARK 500 1 LEU A 64 -172.46 -67.07 REMARK 500 1 ASP A 89 -44.14 -160.47 REMARK 500 1 GLN A 92 -67.53 -132.92 REMARK 500 1 PRO A 95 65.43 -67.41 REMARK 500 1 ARG A 102 95.70 -161.18 REMARK 500 1 PHE A 106 -166.73 -127.73 REMARK 500 1 GLN A 110 21.87 -143.99 REMARK 500 1 MET A 116 -72.98 -134.27 REMARK 500 1 GLN A 142 -31.12 177.79 REMARK 500 1 ASP A 154 -42.91 -169.64 REMARK 500 2 SER A 4 97.24 -175.47 REMARK 500 2 ARG A 5 93.72 -57.50 REMARK 500 2 PRO A 15 31.68 -65.08 REMARK 500 2 GLN A 16 -39.85 -160.41 REMARK 500 2 GLN A 40 166.48 -47.40 REMARK 500 2 GLU A 41 87.67 -56.62 REMARK 500 2 SER A 57 30.86 -142.77 REMARK 500 2 ALA A 63 93.59 179.57 REMARK 500 2 LEU A 64 177.08 -58.79 REMARK 500 2 ASP A 89 -45.92 -152.66 REMARK 500 2 GLN A 92 73.60 -105.27 REMARK 500 2 THR A 94 56.41 -160.26 REMARK 500 2 GLU A 97 107.36 -42.32 REMARK 500 2 GLN A 110 22.32 -148.08 REMARK 500 2 MET A 116 -71.69 -132.99 REMARK 500 2 GLN A 142 -36.30 -177.68 REMARK 500 2 ASP A 154 37.89 -177.80 REMARK 500 3 ALA A 3 -167.21 -112.26 REMARK 500 3 SER A 4 89.56 56.61 REMARK 500 3 ARG A 5 95.83 -62.65 REMARK 500 3 PRO A 15 24.72 -66.95 REMARK 500 3 GLN A 16 -41.27 -160.53 REMARK 500 3 ASN A 33 163.20 179.27 REMARK 500 3 GLU A 41 94.31 -52.25 REMARK 500 3 ALA A 63 96.31 179.54 REMARK 500 3 LEU A 64 -178.37 -62.40 REMARK 500 3 ASP A 89 -45.51 -160.09 REMARK 500 3 GLN A 92 -66.97 -138.66 REMARK 500 3 PRO A 95 62.66 -67.94 REMARK 500 REMARK 500 THIS ENTRY HAS 565 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1IRY A 1 156 UNP P36639 8ODP_HUMAN 1 156 SEQRES 1 A 156 MET GLY ALA SER ARG LEU TYR THR LEU VAL LEU VAL LEU SEQRES 2 A 156 GLN PRO GLN ARG VAL LEU LEU GLY MET LYS LYS ARG GLY SEQRES 3 A 156 PHE GLY ALA GLY ARG TRP ASN GLY PHE GLY GLY LYS VAL SEQRES 4 A 156 GLN GLU GLY GLU THR ILE GLU ASP GLY ALA ARG ARG GLU SEQRES 5 A 156 LEU GLN GLU GLU SER GLY LEU THR VAL ASP ALA LEU HIS SEQRES 6 A 156 LYS VAL GLY GLN ILE VAL PHE GLU PHE VAL GLY GLU PRO SEQRES 7 A 156 GLU LEU MET ASP VAL HIS VAL PHE CYS THR ASP SER ILE SEQRES 8 A 156 GLN GLY THR PRO VAL GLU SER ASP GLU MET ARG PRO CYS SEQRES 9 A 156 TRP PHE GLN LEU ASP GLN ILE PRO PHE LYS ASP MET TRP SEQRES 10 A 156 PRO ASP ASP SER TYR TRP PHE PRO LEU LEU LEU GLN LYS SEQRES 11 A 156 LYS LYS PHE HIS GLY TYR PHE LYS PHE GLN GLY GLN ASP SEQRES 12 A 156 THR ILE LEU ASP TYR THR LEU ARG GLU VAL ASP THR VAL HELIX 1 1 THR A 44 GLY A 58 1 15 HELIX 2 2 ASP A 119 LYS A 130 1 12 SHEET 1 A 5 ARG A 5 VAL A 10 0 SHEET 2 A 5 LEU A 80 PHE A 86 1 O PHE A 86 N LEU A 9 SHEET 3 A 5 LYS A 66 PHE A 74 -1 N PHE A 72 O MET A 81 SHEET 4 A 5 LYS A 132 PHE A 139 1 O PHE A 137 N VAL A 71 SHEET 5 A 5 ILE A 145 VAL A 153 -1 O VAL A 153 N LYS A 132 SHEET 1 B 3 MET A 101 GLN A 107 0 SHEET 2 B 3 ARG A 17 LYS A 23 -1 N VAL A 18 O PHE A 106 SHEET 3 B 3 VAL A 12 LEU A 13 -1 N VAL A 12 O LEU A 19 SHEET 1 C 3 MET A 101 GLN A 107 0 SHEET 2 C 3 ARG A 17 LYS A 23 -1 N VAL A 18 O PHE A 106 SHEET 3 C 3 TRP A 32 ASN A 33 -1 O ASN A 33 N GLY A 21 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