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(-) Description

Title :  NMR STRUCTURE OF UBIQUILIN 1 UBA DOMAIN
 
Authors :  D. Zhang, S. Raasi, D. Fushman
Date :  06 Dec 07  (Deposition) - 18 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Uba, Ubiquilin, Alternative Splicing, Cytoplasm, Nucleus, Phosphoprotein, Proteasome, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Zhang, S. Raasi, D. Fushman
Affinity Makes The Difference: Nonselective Interaction Of The Uba Domain Of Ubiquilin-1 With Monomeric Ubiquitin And Polyubiquitin Chains
J. Mol. Biol. V. 377 162 2008
PubMed-ID: 18241885  |  Reference-DOI: 10.1016/J.JMB.2007.12.029
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUILIN-1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VectorPGEX
    Expression System Vector TypeVECTOR
    FragmentUBA DOMAIN
    GeneUBQLN1, DA41, PLIC1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsPGEX-4T1
    SynonymPROTEIN LINKING IAP WITH CYTOSKELETON 1, PLIC-1, HPLIC- 1

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2JY5)

(-) Sites  (0, 0)

(no "Site" information available for 2JY5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JY5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JY5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JY5)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBAPS50030 Ubiquitin-associated domain (UBA) profile.UBQL1_HUMAN546-586  1A:546-586

(-) Exons   (0, 0)

(no "Exon" information available for 2JY5)

(-) 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:52
 aligned with UBQL1_HUMAN | Q9UMX0 from UniProtKB/Swiss-Prot  Length:589

    Alignment length:92
                                   505       515       525       535       545       555       565       575       585  
          UBQL1_HUMAN   496 GSSGTNGSNATPSENTSPTAGTTEPGHQQFIQQMLQALAGVNPQLQNPEVRFQQQLEQLSAMGFLNREANLQALIATGGDINAAIERLLGSQ 587
               SCOP domains d2                                        jy5a_ A: automated matches                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------UBA-2jy5A01 A:546-583                 ---- Pfam domains
         Sec.struct. author ..----------------------------------------.........hhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------UBA  PDB: A:546-586 UniProt: 546-586     - PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 2jy5 A 536 GS----------------------------------------PEFQNPEVRFQQQLEQLSAMGFLNREANLQALIATGGDINAAIERLLGSS 587
                             |       -         -         -         -  |    545       555       565       575       585  
                             |                                      538                                                 
                           537                                                                                          

   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 2JY5)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: UBA (32)
(-)
Family: UBA (23)

(-) Gene Ontology  (30, 30)

NMR Structure(hide GO term definitions)
Chain A   (UBQL1_HUMAN | Q9UMX0)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    GO:0031593    polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination of the target protein.
    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:0035973    aggrephagy    Selective degradation of protein aggregates by macroautophagy.
    GO:0000045    autophagosome assembly    The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm.
    GO:0097352    autophagosome maturation    Removal of PI3P and Atg8/LC3 after the closure of the phagophore and before the fusion with the endosome/lysosome (e.g. mammals and insects) or vacuole (yeast), and that very likely destabilizes other Atg proteins and thus enables their efficient dissociation and recycling.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0071456    cellular response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0016236    macroautophagy    The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
    GO:1901340    negative regulation of store-operated calcium channel activity    Any process that stops, prevents or reduces the frequency, rate or extent of store-operated calcium channel activity.
    GO:0034140    negative regulation of toll-like receptor 3 signaling pathway    Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 3 signaling pathway.
    GO:1903071    positive regulation of ER-associated ubiquitin-dependent protein catabolic process    Any process that activates or increases the frequency, rate or extent of ER-associated ubiquitin-dependent protein catabolic process.
    GO:0031398    positive regulation of protein ubiquitination    Any process that activates or increases the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:1902175    regulation of oxidative stress-induced intrinsic apoptotic signaling pathway    Any process that modulates the frequency, rate or extent of an oxidative stress-induced intrinsic apoptotic signaling pathway.
    GO:0031396    regulation of protein ubiquitination    Any process that modulates the frequency, rate or extent of the addition of ubiquitin groups to a 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.
    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:0016235    aggresome    An inclusion body formed by dynein-dependent retrograde transport of an aggregated protein on microtubules.
    GO:0005776    autophagosome    A double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the vacuole/lysosome for degradation as part of macroautophagy.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    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.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UBQL1_HUMAN | Q9UMX02jy6 2klc

(-) Related Entries Specified in the PDB File

2jy6