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(-) Description

Title :  CRYSTAL STRUCTURES OF TWO UBC (E2) ENZYMES OF THE UBIQUITIN-CONJUGATING SYSTEM IN CAENORHABDITIS ELEGANS
 
Authors :  N. Schormann, G. Lin, S. Li, J. Symersky, S. Qiu, J. Finley, D. Luo, A. Stanton, M. Carson, M. Luo, Southeast Collaboratory For Structural Genomics (Secsg)
Date :  14 Jul 03  (Deposition) - 22 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.52
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta(4)-Alpha(3), Core, Meander Beta-Sheet Plus One Helix 2, Structural Genomics, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Schormann, G. Lin, S. Li, J. Symersky, S. Qiu, J. Finley, D. Luo, A. Stanton, M. Carson, M. Luo, L. Delucas, P. Pruett, L. Nagy, A. Arabashi, R. Gray, D. Johnson, J. Tsao, B. Bunzel, W. Huang, Q. Shang, C. -H. Luan, S. Lu, J. Zhang, A. Mckinstry, H. Chen
Crystal Structures Of Two Ubc (E2) Enzymes Of The Ubiquitin-Conjugating System In Caenorhabditis Elegans
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE UBIQUITIN-CONJUGATING ENZYME E2-19 KDA
    ChainsA
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneF58A4.10
    Organism ScientificCAENORHABDITIS ELEGANS
    Organism Taxid6239
    SynonymUBIQUITIN-PROTEIN LIGASE, UBIQUITIN CARRIER PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

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(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBC7_CAEEL6-152  1A:6-152
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBC7_CAEEL77-92  1A:77-92

(-) Exons   (0, 0)

(no "Exon" information available for 1PZV)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:152
 aligned with UBC7_CAEEL | P34477 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:161
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163 
           UBC7_CAEEL     4 SSLLLKKQLADMRRVPVDGFSAGLVDDNDIYKWEVLVIGPPDTLYEGGFFKAILDFPRDYPQKPPKMKFISEIWHPNIDKEGNVCISILHDPGDDKWGYERPEERWLPVHTVETILLSVISMLTDPNFESPANVDAAKMQRENYAEFKKKVAQCVRRSQEE 164
               SCOP domains d1pzva_ A: Ubiquitin conjugating enzyme, UBC                                                                                                                      SCOP domains
               CATH domains 1pzvA00 A:4-164 Ubiquitin Conjugating Enzyme                                                                                                                      CATH domains
               Pfam domains ---UQ_con-1pzvA01 A:7-158                                                                                                                                  ------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....eeeee.......eeeeeee..........eeeeeee...hhhhh..eeee................hhhhh..---------.........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --UBIQUITIN_CONJUGAT_2  PDB: A:6-152 UniProt: 6-152                                                                                                  ------------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------UBIQUITIN_CONJUG------------------------------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pzv A   4 SSLLLKKQLADMRRVPVDGFSAGLVDDNDIYKWEVLVIGPPDTLYEGGFFKAILDFPRDYPQKPPKMKFISEIWHPNIDKEGNVCISILHDP---------PEERWLPVHTVETILLSVISMLTDPNFESPANVDAAKMQRENYAEFKKKVAQCVRRSQEE 164
                                    13        23        33        43        53        63        73        83        93 |       - |     113       123       133       143       153       163 
                                                                                                                      95       105                                                           

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  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  (1, 1)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UBC7_CAEEL | P34477)
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: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.
biological process
    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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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