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(-) Description

Title :  THE 1.1A CRYSTALLOGRAPHIC STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME (UBC-2) FROM CAENORHABDITIS ELEGANS: FUNCTIONAL AND EVOLUTIONARY SIGNIFICANCE
 
Authors :  J. A. Gavira, E. Digiamamarino, W. Tempel, Z. J. Liu, B. C. Wang, E. Meehan, J. D. Ng, Southeast Collaboratory For Structural Genomics (Secsg)
Date :  09 Mar 05  (Deposition) - 22 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Psi, Secsg, Ubiquitin-Conjugating Enzyme, Caenorhabditis Elegans, Proteosome Pathway, Structural Genomics, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. Gavira, E. Digiamamarino, W. Tempel, Z. J. Liu, B. C. Wang, E. Meehan, J. D. Ng
The 1. 1A Crystallographic Structure Of Ubiquitin-Conjugating Enzyme (Ubc-2) From Caenorhabditis Elegans: Functional And Evolutionary Significance
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 2
    ChainsA
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneUBC-2, LET-70
    Organism ScientificCAENORHABDITIS ELEGANS
    Organism Taxid6239
    SynonymUBIQUITIN-PROTEIN LIGASE 2, UBIQUITIN CARRIER PROTEIN 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric/Biological Unit (4, 19)
No.NameCountTypeFull Name
1BU32Ligand/Ion(R,R)-2,3-BUTANEDIOL
2CL6Ligand/IonCHLORIDE ION
3NA1Ligand/IonSODIUM ION
4UNX10Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:58 , ASP A:59 , LYS A:63 , UNX A:502BINDING SITE FOR RESIDUE CL A 601
02AC2SOFTWARESER A:-1 , ARG A:131 , LYS A:144 , HOH A:318BINDING SITE FOR RESIDUE CL A 602
03AC3SOFTWAREHIS A:0 , LEU A:3 , ARG A:131 , HOH A:315 , HOH A:356BINDING SITE FOR RESIDUE CL A 603
04AC4SOFTWAREARG A:15BINDING SITE FOR RESIDUE CL A 604
05AC5SOFTWAREGLY A:-2 , HIS A:0 , LYS A:4 , MET A:147BINDING SITE FOR RESIDUE CL A 605
06AC6SOFTWAREBU3 A:201 , HOH A:317 , HOH A:334BINDING SITE FOR RESIDUE CL A 606
07AC7SOFTWARESER A:-1 , ASP A:112 , PRO A:113 , TYR A:127 , BU3 A:201BINDING SITE FOR RESIDUE NA A 701
08AC8SOFTWARESER A:-1 , ASP A:112 , PRO A:113 , PRO A:115 , ASP A:116 , HOH A:319 , HOH A:353 , CL A:606 , NA A:701BINDING SITE FOR RESIDUE BU3 A 201
09AC9SOFTWAREARG A:15 , HOH A:383 , HOH A:404BINDING SITE FOR RESIDUE BU3 A 202
10BC1SOFTWAREASP A:28 , ASP A:29 , LEU A:30 , PHE A:31 , ARG A:139BINDING SITE FOR RESIDUE UNX A 501
11BC2SOFTWARECL A:601BINDING SITE FOR RESIDUE UNX A 502
12BC3SOFTWAREASP A:130BINDING SITE FOR RESIDUE UNX A 503
13BC4SOFTWARESER A:22 , THR A:36BINDING SITE FOR RESIDUE UNX A 504
14BC5SOFTWARELEU A:86 , ASN A:114 , HOH A:364BINDING SITE FOR RESIDUE UNX A 505
15BC6SOFTWAREVAL A:26 , ASP A:29 , SER A:94 , ARG A:139 , UNX A:508 , UNX A:509BINDING SITE FOR RESIDUE UNX A 506
16BC7SOFTWAREGLN A:34 , ALA A:35 , THR A:36BINDING SITE FOR RESIDUE UNX A 507
17BC8SOFTWAREGLY A:27 , ASP A:28 , ALA A:96 , ARG A:139 , UNX A:506BINDING SITE FOR RESIDUE UNX A 508
18BC9SOFTWAREHIS A:32 , SER A:94 , UNX A:506 , UNX A:510BINDING SITE FOR RESIDUE UNX A 509
19CC1SOFTWAREGLN A:136 , UNX A:509BINDING SITE FOR RESIDUE UNX A 510

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z2U)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:60 -Pro A:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_UBC2_CAEEL_001 *H75YUBC2_CAEEL  ---  ---AH75Y
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBC2_CAEEL4-136  1A:4-136
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBC2_CAEEL74-89  1A:74-89

(-) Exons   (0, 0)

(no "Exon" information available for 1Z2U)

(-) 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:150
 aligned with UBC2_CAEEL | P35129 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:150
                               1                                                                                                                                                  
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147
           UBC2_CAEEL     - ---MALKRIQKELQDLGRDPPAQCSAGPVGDDLFHWQATIMGPPESPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRERYNQLAREWTQKYAM 147
               SCOP domains ---d1z2ua1 A:1-147 Ubiquitin conjugating enzyme, UBC                                                                                                   SCOP domains
               CATH domains 1z2uA00 A:-2-147 Ubiquitin Conjugating Enzyme                                                                                                          CATH domains
               Pfam domains -------UQ_con-1z2uA01 A:5-142                                                                                                                    ----- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh....eeeeee..eeeeeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------Y------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------UBIQUITIN_CONJUGAT_2  PDB: A:4-136 UniProt: 4-136                                                                                    ----------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z2u A  -2 GSHMALKRIQKELQDLGRDPPAQCSAGPVGDDLFHWQATIMGPPESPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRERYNQLAREWTQKYAM 147
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147

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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  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UBC2_CAEEL | P35129)
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: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: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.

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