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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UFC1, UFM1 CONJUGATING ENZYME 1
 
Authors :  T. Mizushima, K. Tatsumi, Y. Ozaki, T. Kawakami, A. Suzuki, K. Ogasahara, M. Komatsu, E. Kominami, K. Tanaka, T. Yamane
Date :  06 Aug 07  (Deposition) - 25 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Ufc1, Ufm1, Ubiquitin, Ubl, Polymorphism, Ubl Conjugation Pathway, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Mizushima, K. Tatsumi, Y. Ozaki, T. Kawakami, A. Suzuki, K. Ogasahara, M. Komatsu, E. Kominami, K. Tanaka, T. Yamane
Crystal Structure Of Ufc1, The Ufm1-Conjugating Enzyme
Biochem. Biophys. Res. Commun. V. 362 1079 2007
PubMed-ID: 17825256  |  Reference-DOI: 10.1016/J.BBRC.2007.08.129
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UFM1-CONJUGATING ENZYME 1
    ChainsA
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6P
    Expression System StrainBL21(RIL)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneUFC1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN-FOLD MODIFIER-CONJUGATING ENZYME 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (0, 0)

(no "Site" information available for 2Z6O)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z6O)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:90 -Pro A:91
2Val A:129 -Pro A:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_028312Y90CUFC1_HUMANPolymorphism17849932AY90C

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z6O)

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3aENST000003680033aENSE00001446105chr1:161123542-161123910369UFC1_HUMAN1-41411A:1-4141
1.4aENST000003680034aENSE00000958732chr1:161126740-16112680768UFC1_HUMAN42-64231A:42-6423
1.4cENST000003680034cENSE00001132692chr1:161127044-16112710764UFC1_HUMAN64-85221A:64-8522
1.5aENST000003680035aENSE00001132687chr1:161127407-16112748377UFC1_HUMAN86-111261A:86-11126
1.5dENST000003680035dENSE00001132682chr1:161127911-16112800191UFC1_HUMAN111-141311A:111-14131
1.6bENST000003680036bENSE00001446104chr1:161128202-161128646445UFC1_HUMAN142-167261A:142-16625

(-) 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:166
 aligned with UFC1_HUMAN | Q9Y3C8 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      
           UFC1_HUMAN     1 MADEATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKEGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKICLTDHFKPLWARNVPKFGLAHLMALGLGPWLAVEIPDLIQKGVIQHKEKCN 166
               SCOP domains d2z6oa_ A: Ufm1-conjugating enzyme 1, UFC1                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....eeeeeeeeee..eeeeeeeeee.............hhhhh................hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.....ee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------C---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: A:1-41 UniProt: 1-41     Exon 1.4a  PDB: A:42-64---------------------Exon 1.5a  PDB: A:86-111  ------------------------------Exon 1.6b  PDB: A:142-166 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------Exon 1.4c  PDB: A:64-8-------------------------Exon 1.5d  PDB: A:111-141      ------------------------- Transcript 1 (2)
                 2z6o A   1 MADEATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKEGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKICLTDHFKPLWARNVPKFGLAHLMALGLGPWLAVEIPDLIQKGVIQHKEKCN 166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "CATH Domain" information available for 2Z6O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Z6O)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UFC1_HUMAN | Q9Y3C8)
molecular function
    GO:0071568    UFM1 transferase activity    Catalysis of the transfer of UFM1 from one protein to another via the reaction X-UFM1 + Y --> Y-UFM1 + X, where both X-UFM1 and Y-UFM1 are covalent linkages.
    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).
biological process
    GO:1990592    protein K69-linked ufmylation    A protein ufmylation process in which a polymer of the ubiquitin-like protein UFM1 is formed by linkages between lysine residues at position 69 of the UFM1 monomers, is added to a protein.
    GO:0071569    protein ufmylation    Covalent attachment of the ubiquitin-like protein UFM1 to another protein.
    GO:0034976    response to endoplasmic reticulum stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UFC1_HUMAN | Q9Y3C82k07 2z6p 3evx

(-) Related Entries Specified in the PDB File

2z6p