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(-) Description

Title :  HSP40-YDJ1 DIMERIZATION DOMAIN
 
Authors :  Y. Wu, B. Sha
Date :  26 Aug 04  (Deposition) - 03 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Sheets, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Wu, J. Li, Z. Jin, Z. Fu, B. Sha
The Crystal Structure Of The C-Terminal Fragment Of Yeast Hsp40 Ydj1 Reveals Novel Dimerization Motif For Hsp40
J. Mol. Biol. V. 346 1005 2005
PubMed-ID: 15701512  |  Reference-DOI: 10.1016/J.JMB.2004.12.040
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MITOCHONDRIAL PROTEIN IMPORT PROTEIN MAS5
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentYDJ1 (RESIDUES 258-378)
    GeneMAS5, YDJ1
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymYDJ1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1XAO)

(-) Sites  (0, 0)

(no "Site" information available for 1XAO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XAO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XAO)

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNL064C1YNL064C.1XIV:507099-5058701230MAS5_YEAST1-4094092A:258-378 (gaps)
B:258-378 (gaps)
121
121

(-) 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:115
 aligned with MAS5_YEAST | P25491 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:121
                                   267       277       287       297       307       317       327       337       347       357       367       377 
           MAS5_YEAST   258 SFKRDGDDLVYEAEIDLLTAIAGGEFALEHVSGDWLKVGIVPGEVIAPGMRKVIEGKGMPIPKYGGYGNLIIKFTIKFPENHFTSEENLKKLEEILPPRIVPAIPKKATVDECVLADFDPA 378
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1xaoA01 A:258-337 Urease metallochaperone UreE, N-terminal d      omain         ----------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eeeeeeeeehhhhhhheeeeee.....eeeeee..........eeee......------...eeeeeeee.......hhhhhhhhhhhh.............eeeee.ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:258-378 (gaps) UniProt: 1-409 [INCOMPLETE]                                                               Transcript 1
                 1xao A 258 SFKRDGDDLVYEAEIDLLTAIAGGEFALEHVSGDWLKVGIVPGEVIAPGMRKVIEGKGMP------YGNLIIKFTIKFPENHFTSEENLKKLEEILPPRIVPAIPKKATVDECVLADFDPA 378
                                   267       277       287       297       307       317      |327       337       347       357       367       377 
                                                                                     317    324                                                      

Chain B from PDB  Type:PROTEIN  Length:115
 aligned with MAS5_YEAST | P25491 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:121
                                   267       277       287       297       307       317       327       337       347       357       367       377 
           MAS5_YEAST   258 SFKRDGDDLVYEAEIDLLTAIAGGEFALEHVSGDWLKVGIVPGEVIAPGMRKVIEGKGMPIPKYGGYGNLIIKFTIKFPENHFTSEENLKKLEEILPPRIVPAIPKKATVDECVLADFDPA 378
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1xaoB01 B:258-337 Urease metallochaperone UreE, N-terminal d      omain         ----------------------------------------- CATH domains
           Pfam domains (1) -------DnaJ_C-1xaoB01 B:265-348                                                            ------------------------------ Pfam domains (1)
           Pfam domains (2) -------DnaJ_C-1xaoB02 B:265-348                                                            ------------------------------ Pfam domains (2)
         Sec.struct. author ..eee..eeeeeeeeehhhhhhheeeeee.....eeeeee..........eeee......------...eeeeeeee.......hhhhhhhhhhhh.............eeee..ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:258-378 (gaps) UniProt: 1-409 [INCOMPLETE]                                                               Transcript 1
                 1xao B 258 SFKRDGDDLVYEAEIDLLTAIAGGEFALEHVSGDWLKVGIVPGEVIAPGMRKVIEGKGMP------YGNLIIKFTIKFPENHFTSEENLKKLEEILPPRIVPAIPKKATVDECVLADFDPA 378
                                   267       277       287       297       307       317      |327       337       347       357       367       377 
                                                                                     317    324                                                      

   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  (0, 0)

(no "SCOP Domain" information available for 1XAO)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MAS5_YEAST | P25491)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0001671    ATPase activator activity    Binds to and increases the ATP hydrolysis activity of an ATPase.
    GO:0031072    heat shock protein binding    Interacting selectively and non-covalently with a heat shock protein, any protein synthesized or activated in response to heat shock.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0006458    'de novo' protein folding    The process of assisting in the folding of a nascent peptide chain into its correct tertiary structure.
    GO:0032781    positive regulation of ATPase activity    Any process that activates or increases the rate of ATP hydrolysis by an ATPase.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0042026    protein refolding    The process carried out by a cell that restores the biological activity of an unfolded or misfolded protein, using helper proteins such as chaperones.
    GO:0045047    protein targeting to ER    The process of directing proteins towards the endoplasmic reticulum (ER) using signals contained within the protein. One common mechanism uses a 16- to 30-residue signal sequence, typically located at the N-terminus of the protein and containing positively charged amino acids followed by a continuous stretch of hydrophobic residues, which directs the ribosome to the ER membrane and initiates transport of the growing polypeptide across the ER membrane.
    GO:0006626    protein targeting to mitochondrion    The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0009408    response to heat    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0035719    tRNA import into nucleus    The directed movement of tRNA from the cytoplasm to the nucleus.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor 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.
cellular component
    GO:0072380    TRC complex    An ER membrane insertion complex that contains subunits that recognize two types of transmembrane domain signals. In budding yeast the complex contains Get4p, Get5p, Sgt2p, and at least two heat shock proteins (HSPs).
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MAS5_YEAST | P254911nlt

(-) Related Entries Specified in the PDB File

1c3g TYPE II HSP40-SIS1 PEPTIDE BINDING DOMAIN
1nlt TYPE I HSP40-YDJ1 PEPTIDE BINDING DOMAIN COMPLEXED WITH SUBSTRATE