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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN UBC4 E2 CONJUGATING ENZYME
 
Authors :  R. Benirschke, J. R. Thompson, G. Mer
Date :  14 Dec 09  (Deposition) - 05 May 10  (Release) - 25 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  E2 Conjugating Enzyme, Ubiquitin Ligase, Ubl Conjugation Pathway, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. C. Benirschke, J. R. Thompson, Y. Nomine, E. Wasielewski, N. Juranic, S. Macura, S. Hatakeyama, K. I. Nakayama, M. V. Botuyan, G. Mer
Molecular Basis For The Association Of Human E4B U Box Ubiquitin Ligase With E2-Conjugating Enzymes Ubch5C And Ubc4.
Structure V. 18 955 2010
PubMed-ID: 20696396  |  Reference-DOI: 10.1016/J.STR.2010.04.017

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 D2
    ChainsA
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPT7.7
    Expression System StrainBL21 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-147
    GeneUBE2D2, UBC4, UBCH5B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN-PROTEIN LIGASE D2, UBIQUITIN CARRIER PROTEIN D2, UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2, E2(17)KB 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3L1Y)

(-) Sites  (0, 0)

(no "Site" information available for 3L1Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L1Y)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:60 -Pro A:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L1Y)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2D2_HUMAN4-136  1A:4-136
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UB2D2_HUMAN74-89  1A:74-89

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2dENST000003987342dENSE00002067174chr5:138941311-13894140090UB2D2_HUMAN1-881A:1-88
1.6aENST000003987346aENSE00001727928chr5:138979957-13898002064UB2D2_HUMAN9-30221A:9-3022
1.7aENST000003987347aENSE00000898561chr5:138994171-13899420232UB2D2_HUMAN30-40111A:30-4011
1.8ENST000003987348ENSE00001673964chr5:138994282-13899435978UB2D2_HUMAN41-66261A:41-6626
1.9ENST000003987349ENSE00001785808chr5:138994446-138994551106UB2D2_HUMAN67-102361A:67-10236
1.10bENST0000039873410bENSE00001694979chr5:139002953-13900304694UB2D2_HUMAN102-133321A:102-13332
1.11bENST0000039873411bENSE00002035469chr5:139006341-139006642302UB2D2_HUMAN133-147151A:133-14715
1.11fENST0000039873411fENSE00002075824chr5:139007137-139007271135UB2D2_HUMAN-00--

(-) 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:152
 aligned with UB2D2_HUMAN | P62837 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:152
                                 1                                                                                                                                                  
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145  
          UB2D2_HUMAN     - -----MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
               SCOP domains d3l1ya_ A: Ubiquitin conjugating enzyme, UBC                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------UQ_con-3l1yA01 A:5-142                                                                                                                    ----- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------UBIQUITIN_CONJUGAT_2  PDB: A:4-136 UniProt: 4-136                                                                                    ----------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) -----1.2d    Exon 1.6a  PDB: A:9-30----------Exon 1.8  PDB: A:41-66    -----------------------------------Exon 1.10b  PDB: A:102-133      -------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.7a  --------------------------Exon 1.9  PDB: A:67-102             ------------------------------Exon 1.11b      Transcript 1 (2)
                 3l1y A  -4 HHMNSMALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYQTDREKYNRIAREWTQKYAM 147
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145  

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L1Y)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: UBC (69)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UB2D2_HUMAN | P62837)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0035666    TRIF-dependent toll-like receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the TRIF adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    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:0051865    protein autoubiquitination    The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink.
    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:0061418    regulation of transcription from RNA polymerase II promoter in response to hypoxia    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    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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    Tyr A:60 - Pro A:61   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        UB2D2_HUMAN | P628371ur6 1w4u 2clw 2esk 2eso 2esp 2esq 3a33 3jvz 3jw0 3tgd 3zni 4a49 4a4b 4a4c 4auq 4ddg 4ddi 4ldt 4v3k 4v3l 4wz3 5d0k 5d0m 5d1k 5d1l 5d1m 5edv 5mnj 5ulf 5ulh 5ulk

(-) Related Entries Specified in the PDB File

3l1x CRYSTAL STRUCTURE OF U-BOX DOMAIN OF HUMAN E4B UBIQUITIN LIGASE
3l1z CRYSTAL STRUCTURE OF THE U-BOX DOMAIN OF HUMAN E4B UBIQUITIN LIGASE IN COMPLEX WITH UBCH5C E2 UBIQUITIN CONJUGATING ENZYME