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(-) Description

Title :  UBIQUITIN CONJUGATING ENZYME, UBC13
 
Authors :  A. P. Vandemark, R. M. Hofmann, C. Tsui, C. M. Pickart, C. Wolberger
Date :  03 Jun 01  (Deposition) - 20 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ubiquitin, Ubiquitin-Conjugating Enzyme, E2, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. P. Vandemark, R. M. Hofmann, C. Tsui, C. M. Pickart, C. Wolberger
Molecular Insights Into Polyubiquitin Chain Assembly: Crystal Structure Of The Mms2/Ubc13 Heterodimer.
Cell(Cambridge, Mass. ) V. 105 711 2001
PubMed-ID: 11440714  |  Reference-DOI: 10.1016/S0092-8674(01)00387-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN CONJUGATING ENZYME E2-17.5 KDA
    ChainsA, B
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX
    Expression System StrainBL21PJY2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneUBC13
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    Other DetailsGST-FUSION

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1JBB)

(-) Sites  (0, 0)

(no "Site" information available for 1JBB)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JBB)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:62 -Pro A:63
2Tyr B:62 -Pro B:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JBB)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBC13_YEAST6-138
 
  2A:6-138
B:6-138
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBC13_YEAST76-91
 
  2A:76-91
B:76-91
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBC13_YEAST6-138
 
  1A:6-138
-
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBC13_YEAST76-91
 
  1A:76-91
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBC13_YEAST6-138
 
  1-
B:6-138
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBC13_YEAST76-91
 
  1-
B:76-91

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR092W1YDR092W.1IV:629874-62990330UBC13_YEAST1-10102A:3-10
B:3-10
8
8
1.2YDR092W2YDR092W.2IV:630172-630603432UBC13_YEAST11-1531432A:11-150
B:11-149
140
139

(-) 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:148
 aligned with UBC13_YEAST | P52490 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:148
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        
          UBC13_YEAST     3 SLPKRIIKETEKLVSDPVPGITAEPHDDNLRYFQVTIEGPEQSPYEDGIFELELYLPDDYPMEAPKVRFLTKIYHPNIDRLGRICLDVLKTNWSPALQIRTVLLSIQALLASPNPNDPLANDVAEDWIKNEQGAKAKAREWTKLYAKK 150
               SCOP domains d1jbba_ A: Ubiquitin conjugating enzyme, UBC                                                                                                         SCOP domains
               CATH domains 1jbbA00 A:3-150 Ubiquitin Conjugating Enzyme                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---UBIQUITIN_CONJUGAT_2  PDB: A:6-138 UniProt: 6-138                                                                                    ------------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------UBIQUITIN_CONJUG----------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1Exon 1.2  PDB: A:11-150 UniProt: 11-153 [INCOMPLETE]                                                                                         Transcript 1
                 1jbb A   3 SLPKRIIKETEKLVSDPVPGITAEPHDDNLRYFQVTIEGPEQSPYEDGIFELELYLPDDYPMEAPKVRFLTKIYHPNIDRLGRICLDVLKTNWSPALQIRTVLLSIQALLASPNPNDPLANDVAEDWIKNEQGAKAKAREWTKLYAKK 150
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with UBC13_YEAST | P52490 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:147
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       
          UBC13_YEAST     3 SLPKRIIKETEKLVSDPVPGITAEPHDDNLRYFQVTIEGPEQSPYEDGIFELELYLPDDYPMEAPKVRFLTKIYHPNIDRLGRICLDVLKTNWSPALQIRTVLLSIQALLASPNPNDPLANDVAEDWIKNEQGAKAKAREWTKLYAK 149
               SCOP domains d1jbbb_ B: Ubiquitin conjugating enzyme, UBC                                                                                                        SCOP domains
               CATH domains 1jbbB00 B:3-149 Ubiquitin Conjugating Enzyme                                                                                                        CATH domains
           Pfam domains (1) ----UQ_con-1jbbB01 B:7-144                                                                                                                    ----- Pfam domains (1)
           Pfam domains (2) ----UQ_con-1jbbB02 B:7-144                                                                                                                    ----- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhh....eeeeee..eeeeeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---UBIQUITIN_CONJUGAT_2  PDB: B:6-138 UniProt: 6-138                                                                                    ----------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1Exon 1.2  PDB: B:11-149 UniProt: 11-153 [INCOMPLETE]                                                                                        Transcript 1
                 1jbb B   3 SLPKRIIKETEKLVSDPVPGITAEPHDDNLRYFQVTIEGPEQSPYEDGIFELELYLPDDYPMEAPKVRFLTKIYHPNIDRLGRICLDVLKTNWSPALQIRTVLLSIQALLASPNPNDPLANDVAEDWIKNEQGAKAKAREWTKLYAK 149
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: UBC (69)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (UBC13_YEAST | P52490)
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:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
    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:0010994    free ubiquitin chain polymerization    The process of creating free ubiquitin chains, compounds composed of a large number of ubiquitin monomers. These chains are not conjugated to a protein.
    GO:0006301    postreplication repair    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication.
    GO:0070534    protein K63-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is added to a protein. K63-linked ubiquitination does not target the substrate protein for degradation, but is involved in several pathways, notably as a signal to promote error-free DNA postreplication repair.
    GO:0006513    protein monoubiquitination    Addition of a single ubiquitin group to a protein.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0031371    ubiquitin conjugating enzyme complex    Any complex that possesses ubiquitin conjugating enzyme activity.

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 Related Entries

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

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        UBC13_YEAST | P524901jat 2gmi 4fh1

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