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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DNMT1 AND USP7/HAUSP COMPLEX
 
Authors :  J. Cheng, H. Yang, J. Fang, R. Gong, P. Wang, Z. Li, Y. Xu
Date :  11 Mar 15  (Deposition) - 27 May 15  (Release) - 27 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.92
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Dna Methylation, Deubiquitination, Dna Methyltransferase, Modification, Transferase-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Cheng, H. Yang, J. Fang, L. Ma, R. Gong, P. Wang, Z. Li, Y. Xu
Molecular Mechanism For Usp7-Mediated Dnmt1 Stabilization B Acetylation.
Nat Commun V. 6 7023 2015
PubMed-ID: 25960197  |  Reference-DOI: 10.1038/NCOMMS8023

(-) Compounds

Molecule 1 - DNA (CYTOSINE-5)-METHYLTRANSFERASE 1
    Chains: A
    EC Number: 2.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 600-1600
    Gene: DNMT1, AIM, CXXC9, DNMT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNMT1,CXXC-TYPE ZINC FINGER PROTEIN 9,DNA METHYLTRANSFERASE HSAI,M.HSAI,MCMT
 
Molecule 2 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7
    Chains: C
    EC Number: 3.4.19.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 560-1102
    Gene: USP7, HAUSP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEUBIQUITINATING ENZYME 7,HERPESVIRUS-ASSOCIATED UBIQUITIN- SPECIFIC PROTEASE,UBIQUITIN THIOESTERASE 7,UBIQUITIN-SPECIFIC- PROCESSING PROTEASE 7

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1476 , CYS A:1478 , CYS A:1485 , HIS A:1502binding site for residue ZN A 1701
2AC2SOFTWAREHIS A:793 , CYS A:820 , CYS A:893 , CYS A:896binding site for residue ZN A 1702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YOC)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn C:656 -Pro C:657

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YOC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YOC)

(-) Exons   (0, 0)

(no "Exon" information available for 4YOC)

(-) Sequences/Alignments

Asymmetric/Biological 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:882
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhh................................eeee....ee...eeee.eeee..eeee...eeee.........eeeeeeeeeee...eeeeeeeeeee.hhh.hhhhh...eeeeeeeeeeee...eeeee.eee.....hhhhh..........eeeeeeee....eee...............hhhhhhhhhhhhhh..ee..eeee...eeee.eeee..eeee...eeee....................hhhhhh...........eeeeeeeeeee............eeeeeeeehhhhh..hhhhhh.....eeeeeeeeeeee.hhh.eeeeeee......hhhhhhh....eeeeeeeee....eee..hhhhh.................eeeeee....hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhh...eee..hhhhhhhhhhh..................eeee.............hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh..hhhhhhhhhhhhhhh.eeeeeeee.hhhh.....eeeeeeee................hhhhh...eee..eee...............hhhhhhh............ee.......hhhhhhhhh......ee.......hhhhhhhhhh.......hhhhh....ee.....ee.......................hhhhhh....hhhhh.......hhhhhhhhhhhhhh.....................................hhhhhhhhh..........hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4yoc A  615 PTKATTTKLVYQIFDTFFADEEVDDNIPEMPSPKKMHQGKKKKQNKNRISWVGEAVKTDGKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVKVIYKAPSENWAMEGGMDPESGKTYFYQLWYDQDYARFESPPKTQPTEDNKFKFCVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVYLPPEAFTFNIKLEPVDEDLYPEHYRKYSDYNLDAPEPYRIGRIKEIFCPKKSNGRPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHARSPGNKGKGKGKEIKLPKLRTLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGSTVFTEDCNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNGASALEISYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPLAPGSDWRDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKACDPAARQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAKAIGLEIKLCMLAKA 1600
                                   624       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852||     868       878       888       898       908       918       928       938       948   ||  967       977 ||    991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111   || 1138      1148      1158      1168      1178      1188      1198      1208      1218      1228      1238      1248      1258      1268      1278      1288      1298      1308      1318      1328      1338      1348      1358      1368      1378      1388      1398      1408      1418      1428      1438      1448      1458      1468      1478      1488      1498      1508      1518      1528      1538      1548      1558      1568      1578      1588      1598  
                                            633|                                                                                                                                                    853|                                                                                         952|              979|                                                                                                                               1115|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                             702                                                                                                                                                     860                                                                                          962               984                                                                                                                                1133                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:529
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhh.eeeeeeee.hhh................eeeeee...hhhhhhhhhhhhhh.hhh.eeeeeeee.....eee...........hhhhhh.....eeeeeee.hhhhhh............eeeeeeeeee....eeeeeeeeeee...hhhhhhhhhhhhh.......eeeeeeee..eeee......hhhhhh.......eeeeee.hhhhhhh...hhhhhhhhhhheeeeeeee........eeeeee...hhhhhhhhhhhhhh.hhh.eeeeee......eeee.......hhhhhhh.......eeeeeee...hhhhhhh...eeeeee.....eeeeee......hhhhhhhhhhhhh.........eeeeeee..eeeeee....hhhhh......eeeeee.hhhhhh......eeeeeeee......eeeeeeeeee....hhhhhhhhhhhhhh....hhhhheeeeee..eeee........hhhhh............eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4yoc C  555 GPLGSEAHLYMQVQIVAEDQFCGHQGNDMYDEEKVKYTVFKVLKNSSLAEFVQSLSQTMGFPQDQIRLWPMQARSNGTKRPAMLDNEADGNKTMIELSDNENPWTIFLETVDPELAASGATLPKFDKDHDVMLFLKMYDPKTRSLNYCGHIYTPISCKIRDLLPVMCDRAGFIQDTSLILYEEVKPNLTERIQDYDVSLDKALDELMDGDIIVFQKDDPENDNSELPTAKEYFRDLYHRVDVIFCDKTIPNDPGFVVTLSNRMNYFQVAKTVAQRLNTDPMLLQFFKSQGYRDGPGNPLRHNYEGTLRDLLQFFKPRQPKKLYYQQLKMKITDFENRRSFKCIWLNSQFREEEITLYPDKHGCVRDLLEECKKAVELGEKASGKLRLLEIVSYKIIGVHQEDELLECLSPATSRTFRIEEIPLDQVDIDKENEMLVTVAHFHKEVFGTFGIPFLLRIHQGEHFREVMKRIQSLLDIQEKEFEKFKFAIVMMGRHQYINEDEYEVNLKDFEPQPGNMSHPRPWLGLDHFN 1083
                                   564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4YOC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YOC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YOC)

(-) Gene Ontology  (97, 102)

Asymmetric/Biological Unit(hide GO term definitions)

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  UBP7_HUMAN | Q93009
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 Related Entries

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

UniProtKB/Swiss-Prot
        DNMT1_HUMAN | P26358: 3epz 3pta 3swr 4wxx 4z96 4z97
        UBP7_HUMAN | Q93009: 1nb8 1nbf 1yy6 1yze 2f1w 2f1x 2f1y 2f1z 2foj 2foo 2fop 2kvr 2xxn 2ylm 3mqr 3mqs 4jjq 4kg9 4m5w 4m5x 4pyz 4wph 4wpi 4ysi 4z96 4z97 5c56 5c6d 5fwi 5gg4 5j7t 5jtj 5jtv

(-) Related Entries Specified in the PDB File

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