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(-) Description

Title :  CRYSTAL STRUCTURE OF URM1
 
Authors :  J. Yu, C. Z. Zhou
Date :  07 Jul 07  (Deposition) - 17 Jul 07  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.44
Chains :  Asym./Biol. Unit :  A
Keywords :  Ubiquitin-Like Protein, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Yu, C. Z. Zhou
Crystal Structure Of The Dimeric Urm1 From The Yeast Saccharomyces Cerevisiae.
Proteins V. 71 1050 2008
PubMed-ID: 18260097  |  Reference-DOI: 10.1002/PROT.21975
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN-RELATED MODIFIER 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET29A-DERIVED
    Expression System StrainROSETTA(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneURM1
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    StrainS288C
    SynonymURM1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2058 , HOH A:2079 , HOH A:2085 , HOH A:2102 , HOH A:2114 , HOH A:2158BINDING SITE FOR RESIDUE MG A 1001
2AC2SOFTWAREHOH A:2109 , HOH A:2154 , HOH A:2162 , HOH A:2165 , HOH A:2170 , HOH A:2221BINDING SITE FOR RESIDUE MG A 1002
3AC3SOFTWAREILE A:38 , SER A:60 , ILE A:61 , TRP A:74 , LYS A:80 , HOH A:2067 , HOH A:2179 , HOH A:2185BINDING SITE FOR RESIDUE EDO A 2001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:30 -Pro A:31

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QJL)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YIL008W1YIL008W.1IX:342533-342832300URM1_YEAST1-99991A:1-9999

(-) 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:99
 aligned with URM1_YEAST | P40554 from UniProtKB/Swiss-Prot  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
            URM1_YEAST    1 MVNVKVEFLGGLDAIFGKQRVHKIKMDKEDPVTVGDLIDHIVSTMINNPNDVSIFIEDDSIRPGIITLINDTDWELEGEKDYILEDGDIISFTSTLHGG 99
               SCOP domains d2qjla_ A: automated matches                                                                        SCOP domains
               CATH domains 2qjlA00 A:1-99  [code=3.10.20.30, no name defined]                                                  CATH domains
               Pfam domains --Urm1-2qjlA01 A:3-99                                                                               Pfam domains
         Sec.struct. author .eeeeeeee.hhhhhh....eeeeee......hhhhhhhhhhhhh..hhhhhhhhee..ee...eeeee..ee.hhhhhhhh......eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-99 UniProt: 1-99                                                                 Transcript 1
                  2qjl A  1 MVNVKVEFLGGLDAIFGKQRVHKIKMDKEDPVTVGDLIDHIVSTMINNPNDVSIFIEDDSIRPGIITLINDTDWELEGEKDYILEDGDIISFTSTLHGG 99
                                    10        20        30        40        50        60        70        80        90         

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (URM1_YEAST | P40554)
molecular function
    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).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0031386    protein tag    A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
    GO:0016783    sulfurtransferase activity    Catalysis of the transfer of sulfur atoms from one compound (donor) to another (acceptor).
biological process
    GO:0007114    cell budding    A form of asexual reproduction, occurring in certain bacteria and fungi (e.g. yeasts) and some primitive animals in which an individual arises from a daughter cell formed by pinching off a part of the parent cell. The budlike outgrowths so formed may sometimes remain attached to the parent cell.
    GO:0034599    cellular response to oxidative 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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0001403    invasive growth in response to glucose limitation    A growth pattern exhibited by budding haploid cells under certain growth conditions, in which cells retain the typical axial budding pattern of haploids, but become elongated and fail to separate after division; during growth on a solid substrate, this results in penetration of cells into the agar medium. An example of this process is found in Saccharomyces cerevisiae.
    GO:0032447    protein urmylation    Covalent attachment of the ubiquitin-like protein URM1 to another protein.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    GO:0034227    tRNA thio-modification    The addition a sulfur atom to a nucleotide in a tRNA molecule.
    GO:0002143    tRNA wobble position uridine thiolation    The process in which a uridine residue at position 34 in the anticodon of a tRNA is post-transcriptionally thiolated at the C2 position. This process involves transfer of a sulfur from cysteine to position C2 by several steps.
    GO:0002098    tRNA wobble uridine modification    The process in which a uridine in position 34 of a tRNA is post-transcriptionally modified.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        URM1_YEAST | P405542ax5 2pko

(-) Related Entries Specified in the PDB File

2ax5 SOLUTION STRUCTURE