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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  HUMAN UBC9
Authors :  J. H. Naismith, M. Giraud
Date :  23 Jan 98  (Deposition) - 27 May 98  (Release) - 24 Feb 09  (Revision)
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Sumo Conjugating Enzyme, Ubiquitin Conjugating Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  M. F. Giraud, J. M. Desterro, J. H. Naismith
Structure Of Ubiquitin-Conjugating Enzyme 9 Displays Significant Differences With Other Ubiquitin-Conjugating Enzymes Which May Reflect Its Specificity For Sumo Rather Than Ubiquitin.
Acta Crystallogr. , Sect. D V. 54 891 1998
PubMed-ID: 9757105  |  Reference-DOI: 10.1107/S0907444998002480
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBC9
    EC Number6.3.2.19
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsGST-FUSION
    SynonymUBCH9, UBE9, UBCI

 Structural Features

(-) Chains, Units

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 1A3S)

(-) Sites  (0, 0)

(no "Site" information available for 1A3S)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1A3S)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
1Tyr A:68 -Pro A:69
2Glu A:78 -Pro A:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A3S)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBC9_HUMAN7-146  1A:7-146
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBC9_HUMAN82-97  1A:82-97

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) 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:158
 aligned with UBC9_HUMAN | P63279 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
               SCOP domains d1a3sa_ A: Ubiquitin conjugating enzyme, UBC                                                                                                                   SCOP domains
               CATH domains 1a3sA00 A:1-158 Ubiquitin Conjugating Enzyme                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh......eeee...........eeeeeee..........eeeeeee..........eeee.................hhh...........hhhhhhhhhhhhh.........hhhhhhhhh.hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------UBIQUITIN_CONJUGAT_2  PDB: A:7-146 UniProt: 7-146                                                                                           ------------ PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------UBIQUITIN_CONJUG------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.4b  PDB: A:1-22Exon 1.5  PDB: A:23-50      Exon 1.6a  PDB: A:51-75  ------------------------------------Exon 1.8a  PDB: A:112-138  -------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------Exon 1.7  PDB: A:75-111              --------------------------Exon 1.9c             Transcript 1 (2)
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        

   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  (1, 1)

Asymmetric/Biological Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1A3S)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UBC9_HUMAN | P63279)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0043398    HLH domain binding    Interacting selectively and non-covalently with Helix Loop Helix, a domain of 40-50 residues that occurs in specific DNA-binding proteins that act as transcription factors. The domain is formed of two amphipathic helices joined by a variable length linker region that can form a loop and it mediates protein dimerization.
    GO:0071535    RING-like zinc finger domain binding    Interacting selectively and non-covalently with a RING-like zinc finger domain domain of a protein. The RING-like domain is a zinc finger domain that is related to the C3HC4 RING finger domain.
    GO:0061656    SUMO conjugating enzyme activity    Isoenergetic transfer of SUMO from one protein to another via the reaction X-SUMO + Y -> Y-SUMO + X, where both the X-SUMO and Y-SUMO linkages are thioester bonds between the C-terminal amino acid of SUMO and a sulfhydryl side group of a cysteine residue.
    GO:0019789    SUMO transferase activity    Catalysis of the transfer of SUMO from one protein to another via the reaction X-SUMO + Y --> Y-SUMO + X, where both X-SUMO and Y-SUMO are covalent linkages.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    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.
biological process
    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: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:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0070911    global genome nucleotide-excision repair    The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:1903755    positive regulation of SUMO transferase activity    Any process that activates or increases the frequency, rate or extent of SUMO transferase activity.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
    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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0016605    PML body    A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
    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:0016604    nuclear body    Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    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:1990356    sumoylated E2 ligase complex    A protein complex consisting of a SUMO (small ubiquitin-related modifier) protein bound to a SUMO-conjugating E2 ligase. Sumoylation of the E2 ligase is an intermediate step required for the formation of covalent bonds between a SUMO protein and its ultimate protein target. SUMO is transferred to the E2 ligase by a SUMO-activating E1 enzyme. Sumoylation of the target protein is either facilitated directly by the sumoylated E2 ligase or aided by an optional E3 ligase.
    GO:0000795    synaptonemal complex    A proteinaceous scaffold found between homologous chromosomes during meiosis. It consists of 2 lateral elements and a central element, all running parallel to each other. Transverse filaments connect the lateral elements to the central element.
    GO:1990234    transferase complex    A protein complex capable of catalyzing 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).


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    Glu A:78 - Pro A:79   [ RasMol ]  
    Tyr A:68 - Pro A:69   [ RasMol ]  

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 Related Entries

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

        UBC9_HUMAN | P632791kps 1z5q 1z5s 2grn 2gro 2grp 2grq 2grr 2o25 2pe6 2px9 2xwu 3a4s 3uin 3uio 3uip 4w5v 4y1l 5d2m 5f6d 5f6e 5f6u 5f6v 5f6w 5f6x 5f6y 5fq2

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1A3S)