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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MTH1(G2K MUTANT) IN COMPLEX WITH 2-OXO-DATP
 
Authors :  T. Nakamura, S. Waz, K. Hirata, Y. Nakabeppu, Y. Yamagata
Date :  20 Jun 16  (Deposition) - 04 Jan 17  (Release) - 01 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha-Beta-Alpha Sandwich, Hydrolase, Dna Damage, Dna Repair, Dna Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Waz, T. Nakamura, K. Hirata, Y. Koga-Ogawa, M. Chirifu, T. Arimori, T. Tamada, S. Ikemizu, Y. Nakabeppu, Y. Yamagata
Structural And Kinetic Studies Of The Human Nudix Hydrolase Mth1 Reveal The Mechanism For Its Broad Substrate Specificity
J. Biol. Chem. V. 292 2785 2017
PubMed-ID: 28035004  |  Reference-DOI: 10.1074/JBC.M116.749713
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
    ChainsA, B
    EC Number3.6.1.55, 3.6.1.56
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET8C
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 42-197
    GeneNUDT1, MTH1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMUTT HOMOLOGUE-1,2-HYDROXY-DATP DIPHOSPHATASE,8-OXO-DGTPASE, NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 1,NUDIX MOTIF 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
16U42Ligand/Ion[[(2R,3S,5R)-5-(6-AZANYL-2-OXIDANYLIDENE-1H-PURIN-9-YL)-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE
2NA3Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
16U41Ligand/Ion[[(2R,3S,5R)-5-(6-AZANYL-2-OXIDANYLIDENE-1H-PURIN-9-YL)-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
16U41Ligand/Ion[[(2R,3S,5R)-5-(6-AZANYL-2-OXIDANYLIDENE-1H-PURIN-9-YL)-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:7 , THR A:8 , LEU A:9 , ASN A:33 , GLY A:36 , GLY A:37 , LYS A:38 , PHE A:72 , MET A:81 , TRP A:117 , ASP A:119 , ASP A:120 , TRP A:123 , NA A:202 , NA A:203 , HOH A:309 , HOH A:316 , HOH A:318 , HOH A:319 , HOH A:322 , HOH A:367 , HOH A:370 , HOH A:371 , HOH A:374 , HOH A:378 , HOH A:397 , HOH A:416 , HOH A:447 , HOH B:447binding site for residue 6U4 A 201
2AC2SOFTWAREGLU A:52 , 6U4 A:201 , HOH A:309 , HOH A:322 , HOH A:366 , HOH A:383binding site for residue NA A 202
3AC3SOFTWAREGLY A:36 , GLU A:56 , 6U4 A:201 , HOH A:367 , HOH A:378 , HOH A:382binding site for residue NA A 203
4AC4SOFTWARETYR B:7 , THR B:8 , LEU B:9 , LYS B:23 , ASN B:33 , GLY B:36 , GLY B:37 , LYS B:38 , PHE B:72 , MET B:81 , TRP B:117 , ASP B:119 , ASP B:120 , TRP B:123 , NA B:202 , HOH B:305 , HOH B:330 , HOH B:409 , HOH B:418binding site for residue 6U4 B 201
5AC5SOFTWAREGLY B:36 , GLU B:56 , 6U4 B:201 , HOH B:342binding site for residue NA B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GHJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5GHJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GHJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GHJ)

(-) Exons   (0, 0)

(no "Exon" information available for 5GHJ)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeee...eeeeeee........ee..........hhhhhhhhhhhhhhh......eeeeeeeeee.....eeeeeeeee............eeeeeee....hhhhhhhhhhhhhhhhhh..eeeeeeeee...eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ghj A   1 MKASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV 156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      

Chain B from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeee...eeeeeee........ee..........hhhhhhhhhhhhhhh.eeeeeeeeeeeeeee.....eeeeeeeeeeeee........eeeeeee....hhhhhhhhhhhhhhhhhh..eeeeeeeee...eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ghj B   1 MKASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV 156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      

   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5GHJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GHJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GHJ)

(-) Gene Ontology  (26, 26)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        8ODP_HUMAN | P366391iry 3q93 3whw 3zr0 3zr1 4c9w 4c9x 4n1t 4n1u 5ans 5ant 5anu 5anv 5anw 5fsi 5fsk 5fsl 5fsm 5fsn 5fso 5ghi 5ghm 5ghn 5gho 5ghp 5ghq 5ws7

(-) Related Entries Specified in the PDB File

5ghi 5ghm 5ghn 5gho 5ghp 5ghq