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(-) Description

Title :  CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE UBIQUITIN CONJUGATING ENZYME 1
 
Authors :  M. Glover, R. S. Williams
Date :  04 Oct 00  (Deposition) - 04 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha-Beta Roll, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. S. Hamilton, M. J. Ellison, K. R. Barber, R. S. Williams, J. T. Huzil, S. Mckenna, C. Ptak, M. Glover, G. S. Shaw
Structure Of A Conjugating Enzyme-Ubiquitin Thiolester Intermediate Reveals A Novel Role For The Ubiquitin Tail.
Structure V. 9 897 2001
PubMed-ID: 11591345  |  Reference-DOI: 10.1016/S0969-2126(01)00657-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2-24 KDA
    ChainsA, B
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 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 1FZY)

(-) Sites  (0, 0)

(no "Site" information available for 1FZY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:62 -Pro A:63
2Tyr B:62 -Pro B:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBC1_YEAST5-139
 
  2A:5-139
B:5-139
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBC1_YEAST76-92
 
  2A:76-92
B:76-92
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBC1_YEAST5-139
 
  1A:5-139
-
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBC1_YEAST76-92
 
  1A:76-92
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBC1_YEAST5-139
 
  1-
B:5-139
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBC1_YEAST76-92
 
  1-
B:76-92

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR177W1YDR177W.1IV:816876-817523648UBC1_YEAST1-2152152A:2-150
B:2-150
149
149

(-) 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:149
 aligned with UBC1_YEAST | P21734 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
           UBC1_YEAST     2 SRAKRIMKEIQAVKDDPAAHITLEFVSESDIHHLKGTFLGPPGTPYEGGKFVVDIEVPMEYPFKPPKMQFDTKVYHPNISSVTGAICLDILKNAWSPVITLKSALISLQALLQSPEPNDPQDAEVAQHYLRDRESFNKTAALWTRLYAS 150
               SCOP domains d1fzya_ A: Ubiquitin conjugating enzyme, UBC                                                                                                          SCOP domains
               CATH domains 1fzyA00 A:2-150 Ubiquitin Conjugating Enzyme                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.eeeee.......eeeeeee..........eeeeeee...........................................hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---UBIQUITIN_CONJUGAT_2  PDB: A:5-139 UniProt: 5-139                                                                                      ----------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------UBIQUITIN_CONJUGA---------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:2-150 UniProt: 1-215 [INCOMPLETE]                                                                                                    Transcript 1
                 1fzy A   2 SRAKRIMKEIQAVKDDPAAHITLEFVSESDIHHLKGTFLGPPGTPYEGGKFVVDIEVPMEYPFKPPKMQFDTKVYHPNISSVTGAICLDILKNAWSPVITLKSALISLQALLQSPEPNDPQDAEVAQHYLRDRESFNKTAALWTRLYAS 150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with UBC1_YEAST | P21734 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
           UBC1_YEAST     2 SRAKRIMKEIQAVKDDPAAHITLEFVSESDIHHLKGTFLGPPGTPYEGGKFVVDIEVPMEYPFKPPKMQFDTKVYHPNISSVTGAICLDILKNAWSPVITLKSALISLQALLQSPEPNDPQDAEVAQHYLRDRESFNKTAALWTRLYAS 150
               SCOP domains d1fzyb_ B: Ubiquitin conjugating enzyme, UBC                                                                                                          SCOP domains
               CATH domains 1fzyB00 B:2-150 Ubiquitin Conjugating Enzyme                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.eeee.......eeeeeee...........................eeee.............................hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---UBIQUITIN_CONJUGAT_2  PDB: B:5-139 UniProt: 5-139                                                                                      ----------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------UBIQUITIN_CONJUGA---------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:2-150 UniProt: 1-215 [INCOMPLETE]                                                                                                    Transcript 1
                 1fzy B   2 SRAKRIMKEIQAVKDDPAAHITLEFVSESDIHHLKGTFLGPPGTPYEGGKFVVDIEVPMEYPFKPPKMQFDTKVYHPNISSVTGAICLDILKNAWSPVITLKSALISLQALLQSPEPNDPQDAEVAQHYLRDRESFNKTAALWTRLYAS 150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         

   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 1FZY)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (UBC1_YEAST | P21734)
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.
    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: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: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:0030433    ubiquitin-dependent ERAD pathway    The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
    GO:0016050    vesicle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle.
cellular component
    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.
    GO:0000502    proteasome complex    A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.

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 Related Entries

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

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        UBC1_YEAST | P217341fxt 1tte

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