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(-) Description

Title :  DISTINCT FUNCTIONAL DOMAINS OF UBC9 DICTATE CELL SURVIVAL AND RESISTANCE TO GENOTOXIC STRESS
 
Authors :  R. C. Van Waardenburg, D. M. Duda, C. S. Lancaster, B. A. Schulman, M. A. Bjornsti
Date :  30 Mar 06  (Deposition) - 04 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ubc9P, E2, Smt3, Saccharomyces Cerevisiae, Crystallography, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. C. Van Waardenburg, D. M. Duda, C. S. Lancaster, B. A. Schulman, M. A. Bjornsti
Distinct Functional Domains Of Ubc9 Dictate Cell Survival And Resistance To Genotoxic Stress.
Mol. Cell. Biol. V. 26 4958 2006
PubMed-ID: 16782883  |  Reference-DOI: 10.1128/MCB.00160-06
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2-18 KDA
    ChainsA, B, C, D
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX
    Expression System StrainBL21(DE3)GOLD
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneUBC9
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymUBIQUITIN- PROTEIN LIGASE, UBIQUITIN CARRIER PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2GJD)

(-) Sites  (0, 0)

(no "Site" information available for 2GJD)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GJD)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:68 -Pro A:69
2Tyr B:68 -Pro B:69
3Tyr C:68 -Pro C:69
4Tyr D:68 -Pro D:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GJD)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBC9_YEAST7-146
 
 
 
  4A:7-146
B:7-146
C:7-146
D:7-146
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBC9_YEAST82-97
 
 
 
  4A:82-97
B:82-97
C:82-97
D:82-97

(-) Exons   (2, 8)

Asymmetric/Biological Unit (2, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDL064W1YDL064W.1IV:337487-33752438UBC9_YEAST1-13134A:3-13
B:2-13
C:3-13
D:3-13
11
12
11
11
1.2YDL064W2YDL064W.2IV:337635-338070436UBC9_YEAST13-1571454A:13-157
B:13-157
C:13-157
D:13-157
145
145
145
145

(-) 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:155
 aligned with UBC9_YEAST | P50623 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     
           UBC9_YEAST     3 SLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK 157
               SCOP domains d2gjda_ A: Ubiquitin conjugating enzyme, UBC                                                                                                                SCOP domains
               CATH domains 2gjdA00 A:3-157 Ubiquitin Conjugating Enzyme                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.....eeeeee.....eeeeeeeeeee..........eeeeeee..........eee.................hhhhh.........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.. 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 1.1   ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.2  PDB: A:13-157 UniProt: 13-157                                                                                                           Transcript 1 (2)
                 2gjd A   3 SLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK 157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     

Chain B from PDB  Type:PROTEIN  Length:156
 aligned with UBC9_YEAST | P50623 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
           UBC9_YEAST     2 SSLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK 157
               SCOP domains d2gjdb_ B: Ubiquitin conjugating enzyme, UBC                                                                                                                 SCOP domains
               CATH domains 2gjdB00 B:2-157 Ubiquitin Conjugating Enzyme                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.....eeeeee.....eeeeeeeeeee..........eeeeeee..........eee.................hhhhh.........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----UBIQUITIN_CONJUGAT_2  PDB: B:7-146 UniProt: 7-146                                                                                           ----------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------UBIQUITIN_CONJUG------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.1    ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.2  PDB: B:13-157 UniProt: 13-157                                                                                                           Transcript 1 (2)
                 2gjd B   2 SSLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK 157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      

Chain C from PDB  Type:PROTEIN  Length:155
 aligned with UBC9_YEAST | P50623 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     
           UBC9_YEAST     3 SLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK 157
               SCOP domains d2gjdc_ C: Ubiquitin conjugating enzyme, UBC                                                                                                                SCOP domains
               CATH domains 2gjdC00 C:3-157 Ubiquitin Conjugating Enzyme                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....eeeeee.....eeeeeeeeeee..........eeeeeee..........eee.................hhhhh.........hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----UBIQUITIN_CONJUGAT_2  PDB: C:7-146 UniProt: 7-146                                                                                           ----------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------UBIQUITIN_CONJUG------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.1   ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.2  PDB: C:13-157 UniProt: 13-157                                                                                                           Transcript 1 (2)
                 2gjd C   3 SLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK 157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     

Chain D from PDB  Type:PROTEIN  Length:155
 aligned with UBC9_YEAST | P50623 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     
           UBC9_YEAST     3 SLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK 157
               SCOP domains d2gjdd_ D: Ubiquitin conjugating enzyme, UBC                                                                                                                SCOP domains
               CATH domains 2gjdD00 D:3-157 Ubiquitin Conjugating Enzyme                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.....eeeeee.....eeeeeeeeeee..........eeeeeee..........eee.................hhhhh.........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----UBIQUITIN_CONJUGAT_2  PDB: D:7-146 UniProt: 7-146                                                                                           ----------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------UBIQUITIN_CONJUG------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.1   ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.2  PDB: D:13-157 UniProt: 13-157                                                                                                           Transcript 1 (2)
                 2gjd D   3 SLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK 157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GJD)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (UBC9_YEAST | P50623)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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: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:0000022    mitotic spindle elongation    The cell cycle process in which the distance is lengthened between poles of the mitotic spindle. Mitotic spindle elongation begins during mitotic prophase and ends during mitotic anaphase B.
    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.
cellular component
    GO:0000794    condensed nuclear chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
    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.

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    Tyr A:68 - Pro A:69   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        UBC9_YEAST | P506232eke 3ong 5jne

(-) Related Entries Specified in the PDB File

1a3s CRYSTAL STRUCTURE OF HUMAN UBC9
1u9a CRYSTAL STRUCTURE OF HUMAN UBIQUITIN-CONJUGATING ENZYME UBC9