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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MITOTIC-SPECIFIC UBIQUITIN-CONJUGATING ENZYME, UBCH10
 
Authors :  R. Basavappa, Y. Lin
Date :  09 Mar 01  (Deposition) - 04 Apr 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ubiquitin Conjugating Enzyme, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Lin, W. C. Hwang, R. Basavappa
Structural And Functional Analysis Of The Human Mitotic-Specific Ubiquitin-Conjugating Enzyme, Ubch10.
J. Biol. Chem. V. 277 21913 2002
PubMed-ID: 11927573  |  Reference-DOI: 10.1074/JBC.M109398200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 H10
    ChainsA, B
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPT7-7
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneUBCH10
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN-CONJUGATING ENZYME UBCH10

 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 1I7K)

(-) Sites  (0, 0)

(no "Site" information available for 1I7K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I7K)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:89 -Pro A:90
2Tyr B:89 -Pro B:90

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I7K)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBE2C_HUMAN33-158
 
  2A:33-158
B:33-158
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBE2C_HUMAN103-118
 
  2A:103-118
B:103-118
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBE2C_HUMAN33-158
 
  1A:33-158
-
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBE2C_HUMAN103-118
 
  1A:103-118
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBE2C_HUMAN33-158
 
  1-
B:33-158
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBE2C_HUMAN103-118
 
  1-
B:103-118

(-) Exons   (6, 12)

Asymmetric Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003564551aENSE00001902808chr20:44441215-44441435221UBE2C_HUMAN1-34342A:30-34
B:30-34
5
5
1.1hENST000003564551hENSE00001657265chr20:44442076-4444210328UBE2C_HUMAN34-43102A:34-43
B:34-43
10
10
1.2aENST000003564552aENSE00000845041chr20:44443023-4444310987UBE2C_HUMAN44-72292A:44-72
B:44-72
29
29
1.3cENST000003564553cENSE00001258938chr20:44444180-44444384205UBE2C_HUMAN73-141692A:73-141
B:73-141
69
69
1.4ENST000003564554ENSE00001619811chr20:44444493-4444455260UBE2C_HUMAN141-161212A:141-161
B:141-161
21
21
1.5dENST000003564555dENSE00001893699chr20:44445348-44445596249UBE2C_HUMAN161-179192A:161-175
B:161-175
15
15

(-) 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:146
 aligned with UBE2C_HUMAN | O00762 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:146
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169      
          UBE2C_HUMAN    30 PVGKRLQQELMTLMMSGDKGISAFPESDNLFKWVGTIHGAAGTVYEDLRYKLSLEFPSGYPYNAPTVKFLTPCYHPNVDTQGNICLDILKEKWSALYDVRTILLSIQSLLGEPNIDSPLNTHAAELWKNPTAFKKYLQETYSKQVT 175
               SCOP domains d1i7ka_ A: Ubiquitin conjugating enzyme, UBC                                                                                                       SCOP domains
               CATH domains 1i7kA00 A:30-175 Ubiquitin Conjugating Enzyme                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...eeeeee..eeeeeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---UBIQUITIN_CONJUGAT_2  PDB: A:33-158 UniProt: 33-158                                                                           ----------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------UBIQUITIN_CONJUG--------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1a ---------Exon 1.2a  PDB: A:44-72      Exon 1.3c  PDB: A:73-141 UniProt: 73-141                             -------------------Exon 1.5d       Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.1h -------------------------------------------------------------------------------------------------Exon 1.4             -------------- Transcript 1 (2)
                 1i7k A  30 PVGKRLQQELMTLMMSGDKGISAFPESDNLFKWVGTIHGAAGTVYEDLRYKLSLEFPSGYPYNAPTVKFLTPCYHPNVDTQGNISLDILKEKWSALYDVRTILLSIQSLLGEPNIDSPLNTHAAELWKNPTAFKKYLQETYSKQVT 175
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169      

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with UBE2C_HUMAN | O00762 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:146
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169      
          UBE2C_HUMAN    30 PVGKRLQQELMTLMMSGDKGISAFPESDNLFKWVGTIHGAAGTVYEDLRYKLSLEFPSGYPYNAPTVKFLTPCYHPNVDTQGNICLDILKEKWSALYDVRTILLSIQSLLGEPNIDSPLNTHAAELWKNPTAFKKYLQETYSKQVT 175
               SCOP domains d1i7kb_ B: Ubiquitin conjugating enzyme, UBC                                                                                                       SCOP domains
               CATH domains 1i7kB00 B:30-175 Ubiquitin Conjugating Enzyme                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...eeeeee..eeeeeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---UBIQUITIN_CONJUGAT_2  PDB: B:33-158 UniProt: 33-158                                                                           ----------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------UBIQUITIN_CONJUG--------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1a ---------Exon 1.2a  PDB: B:44-72      Exon 1.3c  PDB: B:73-141 UniProt: 73-141                             -------------------Exon 1.5d       Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.1h -------------------------------------------------------------------------------------------------Exon 1.4             -------------- Transcript 1 (2)
                 1i7k B  30 PVGKRLQQELMTLMMSGDKGISAFPESDNLFKWVGTIHGAAGTVYEDLRYKLSLEFPSGYPYNAPTVKFLTPCYHPNVDTQGNISLDILKEKWSALYDVRTILLSIQSLLGEPNIDSPLNTHAAELWKNPTAFKKYLQETYSKQVT 175
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169      

   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  (0, 0)

(no "Pfam Domain" information available for 1I7K)

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (UBE2C_HUMAN | O00762)
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: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: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:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0010458    exit from mitosis    The cell cycle transition where a cell leaves M phase and enters a new G1 phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place.
    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: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:0031536    positive regulation of exit from mitosis    Any process that activates or increases the rate of progression from anaphase/telophase (high mitotic CDK activity) to G1 (low mitotic CDK activity).
    GO:1904668    positive regulation of ubiquitin protein ligase activity    Any process that activates or increases the frequency, rate or extent of ubiquitin protein ligase activity.
    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:0070979    protein K11-linked ubiquitination    A protein ubiquitination process in which ubiquitin monomers are attached to a protein, and then ubiquitin polymers are formed by linkages between lysine residues at position 11 of the ubiquitin monomers. K11-linked polyubiquitination targets the substrate protein for degradation. The anaphase-promoting complex promotes the degradation of mitotic regulators by assembling K11-linked polyubiquitin chains.
    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: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:0030071    regulation of mitotic metaphase/anaphase transition    Any process that modulates the frequency, rate or extent of the cell cycle process in which a cell progresses from metaphase to anaphase during mitosis, triggered by the activation of the anaphase promoting complex by Cdc20/Sleepy homolog which results in the degradation of Securin.
    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:0005680    anaphase-promoting complex    A ubiquitin ligase complex that degrades mitotic cyclins and anaphase inhibitory protein, thereby triggering sister chromatid separation and exit from mitosis. Substrate recognition by APC occurs through degradation signals, the most common of which is termed the Dbox degradation motif, originally discovered in cyclin B.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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        UBE2C_HUMAN | O007624yii 5a31 5khr 5l9u

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