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(-) Description

Title :  SOLUTION NMR STRUCTURE OF HUMAN E2-LIKE UBIQUITIN-FOLD MODIFIER CONJUGATING ENZYME 1 (UFC1). NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR41
 
Authors :  G. Liu, A. Eletsky, H. S. Atreya, J. M. Aramini, R. Xiao, T. Acton, G. T. Montelione, T. Szyperski, Northeast Structural Genomics Consortium (Nesg)
Date :  25 Jan 08  (Deposition) - 19 Feb 08  (Release) - 29 Sep 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Ufc1, Ubiquitin Conjugating Enzyme, E2, Ufm1, Polymorphism, Ubl Conjugation Pathway, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Liu, F. Forouhar, A. Eletsky, H. S. Atreya, J. M. Aramini, R. Xiao, Y. J. Huang, M. Abashidze, J. Seetharaman, J. Liu, B. Rost, T. Acton, G. T. Montelione, J. F. Hunt, T. Szyperski
Nmr And X-Ray Structures Of Human E2-Like Ubiquitin-Fold Modifier Conjugating Enzyme 1 (Ufc1) Reveal Structural And Functional Conservation In The Metazoan Ufm1-Uba5-Ufc1 Ubiquination Pathway.
J. Struct. Funct. Genom. V. 10 127 2009
PubMed-ID: 19101823  |  Reference-DOI: 10.1007/S10969-008-9054-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UFM1-CONJUGATING ENZYME 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET21
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneUFC1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN-FOLD MODIFIER-CONJUGATING ENZYME 1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2K07)

(-) Sites  (0, 0)

(no "Site" information available for 2K07)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K07)

(-) Cis Peptide Bonds  (2, 40)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Tyr A:90 -Pro A:91
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Val A:129 -Pro A:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (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 2K07)

(-) Exons   (6, 6)

NMR Structure (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:142-16726

(-) Sequences/Alignments

NMR Structure
   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:175
 aligned with UFC1_HUMAN | Q9Y3C8 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:175
                                                                                                                                                                                                167        
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      |  -     
           UFC1_HUMAN     1 MADEATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKEGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKICLTDHFKPLWARNVPKFGLAHLMALGLGPWLAVEIPDLIQKGVIQHKEKCNQ--------   -
               SCOP domains d2k07a_ A: Ufm1-conjugating enzyme 1, UFC1                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....eeeeeeeeee..eeeeeeeeee..................................hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh................... 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:142-167 -------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------Exon 1.4c  PDB: A:64-8-------------------------Exon 1.5d  PDB: A:111-141      ---------------------------------- Transcript 1 (2)
                 2k07 A   1 MADEATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKEGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKICLTDHFKPLWARNVPKFGLAHLMALGLGPWLAVEIPDLIQKGVIQHKEKCNQLEHHHHHH 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     

   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, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2K07)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2K07)

(-) Gene Ontology  (6, 6)

NMR Structure(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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    Tyr A:90 - Pro A:91   [ RasMol ]  
    Val A:129 - Pro A:130   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        UFC1_HUMAN | Q9Y3C82z6o 2z6p 3evx

(-) Related Entries Specified in the PDB File

hr41
6546