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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN UBIQUITIN-CONJUGATING ENZYME E2 E1
 
Authors :  J. R. Walker, G. V. Avvakumov, S. Xue, Y. Li, J. Weigelt, C. H. Arrowsmith A. M. Edwards, A. Bochkarev, S. Dhe-Paganon, Structural Genomics C (Sgc)
Date :  18 Jan 08  (Deposition) - 26 Feb 08  (Release) - 28 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics Consortium, Ubiquitin, Ubiquitin-Conjugating Enzyme, Ligase, Sgc, Ubl Conjugation Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Sheng, J. H. Hong, R. Doherty, T. Srikumar, J. Shloush, G. V. Avvakumov, J. R. Walker, S. Xue, D. Neculai, J. W. Wan, S. K. Kim, C. H. Arrowsmith, B. Raught, S. Dhe-Paganon
A Human Ubiquitin Conjugating Enzyme (E2)-Hect E3 Ligase Structure-Function Screen.
Mol Cell Proteomics V. 11 329 2012
PubMed-ID: 22496338  |  Reference-DOI: 10.1074/MCP.O111.013706

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 E1
    ChainsA
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneUBE2E1, UBCH6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN-PROTEIN LIGASE E1, UBIQUITIN CARRIER PROTEIN E1, UBCH6

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:112 , ILE A:130 , LEU A:135 , HOH A:215 , HOH A:258BINDING SITE FOR RESIDUE GOL A 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BZH)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:106 -Pro A:107

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_061868E25DUB2E1_HUMANPolymorphism36060625AE25D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_061868E25DUB2E1_HUMANPolymorphism36060625AE25D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2E1_HUMAN50-182  1A:50-182
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UB2E1_HUMAN120-135  1A:120-135
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2E1_HUMAN50-182  2A:50-182
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UB2E1_HUMAN120-135  2A:120-135

(-) Exons   (5, 5)

Asymmetric Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003066271aENSE00001810272chr3:23847394-23847579186UB2E1_HUMAN-00--
1.2bENST000003066272bENSE00002168375chr3:23848728-23848912185UB2E1_HUMAN1-51511A:21-51 (gaps)31
1.6bENST000003066276bENSE00001640993chr3:23852951-2385300151UB2E1_HUMAN51-68181A:51-6818
1.8aENST000003066278aENSE00001753310chr3:23929058-23929190133UB2E1_HUMAN68-112451A:68-11245
1.10bENST0000030662710bENSE00001702254chr3:23930603-23930750148UB2E1_HUMAN113-162501A:113-16250
1.11dENST0000030662711dENSE00001631307chr3:23932000-23932807808UB2E1_HUMAN162-193321A:162-19332

(-) 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:161
 aligned with UB2E1_HUMAN | P51965 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:173
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   
          UB2E1_HUMAN    21 QTEKETNTPKKKESKVSMSKNSKLLSTSAKRIQKELADITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFTPEYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT 193
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..------------.hhhhhhhhhhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----D------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------------------------UBIQUITIN_CONJUGAT_2  PDB: A:50-182 UniProt: 50-182                                                                                  ----------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2b  PDB: A:21-51 (gaps) ----------------Exon 1.8a  PDB: A:68-112 UniProt: 68-112     Exon 1.10b  PDB: A:113-162 UniProt: 113-162       ------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.6b         ---------------------------------------------------------------------------------------------Exon 1.11d  PDB: A:162-193       Transcript 1 (2)
                 3bzh A  21 QTEKETN------------KNSKLLSTSAKRIQKELADITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFTPEYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT 193
                                  |  -        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   
                                 27           40                                                                                                                                                         

   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 3BZH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3BZH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BZH)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A   (UB2E1_HUMAN | P51965)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042296    ISG15 transferase activity    Catalysis of the transfer of ISG15 from one protein to another via the reaction X-ISG15 + Y --> Y-ISG15 + X, where both X-ISG15 and Y-ISG15 are covalent linkages.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0061631    ubiquitin conjugating enzyme activity    Isoenergetic transfer of ubiquitin from one protein to another via the reaction X-ubiquitin + Y -> Y-ubiquitin + X, where both the X-ubiquitin and Y-ubiquitin linkages are thioester bonds between the C-terminal glycine of ubiquitin and a sulfhydryl side group of a cysteine residue.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
    GO:0032020    ISG15-protein conjugation    The covalent addition to a protein of ISG15, a ubiquitin-like protein.
    GO:0031145    anaphase-promoting complex-dependent catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, with ubiquitin-protein ligation catalyzed by the anaphase-promoting complex, and mediated by the proteasome.
    GO:0033523    histone H2B ubiquitination    The modification of histone H2B by addition of ubiquitin groups.
    GO:0010390    histone monoubiquitination    The modification of histones by addition of a single ubiquitin group.
    GO:0051436    negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle    Any process that stops, prevents, or reduces the frequency, rate or extent of ubiquitin ligase activity that contributes to the mitotic cell cycle.
    GO:0051437    positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition    Any process that activates, maintains or increases the rate of ubiquitin ligase activity that contributes to the regulation of the mitotic cell cycle phase transition.
    GO:0043161    proteasome-mediated ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0070936    protein K48-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is added to a protein. K48-linked ubiquitination targets the substrate protein for degradation.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042787    protein ubiquitination involved in ubiquitin-dependent protein catabolic process    The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
    GO:0051439    regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle    A cell cycle process that modulates the frequency, rate or extent of ubiquitin ligase activity that contributes to the mitotic cell cycle.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0000151    ubiquitin ligase complex    A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

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 Related Entries

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        UB2E1_HUMAN | P519651xr9 4jjq

(-) Related Entries Specified in the PDB File

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