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(-) Description

Title :  SOLUTION STRUCTURE OF E4B/UFD2A U-BOX DOMAIN
 
Authors :  Y. Nomine, E. Wasielewski, M. Botuyan, G. Mer
Date :  16 Dec 09  (Deposition) - 29 Dec 09  (Release) - 25 Aug 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  U-Box Domain, E3 Ubiquitin Ligase, E4 Polyubiquitin Chain Elongation Factor, Phosphoprotein, Ubl Conjugation Pathway, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. C. Benirschke, J. R. Thompson, Y. Nomine, E. Wasielewski, N. Juranic, S. Macura, S. Hatakeyama, K. I. Nakayama, M. V. Botuyan, G. Mer
Molecular Basis For The Association Of Human E4B U Box Ubiquitin Ligase With E2-Conjugating Enzymes Ubch5C And Ubc4.
Structure V. 18 955 2010
PubMed-ID: 20696396  |  Reference-DOI: 10.1016/J.STR.2010.04.017

(-) Compounds

Molecule 1 - UBIQUITIN CONJUGATION FACTOR E4 B
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System VectorPET15B
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1208-1302
    GeneHDNB1, KIAA0684, UBE4B, UFD2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN FUSION DEGRADATION PROTEIN 2, HOMOZYGOUSLY DELETED IN NEUROBLASTOMA 1

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2KRE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_BOXPS51698 U-box domain profile.UBE4B_HUMAN1227-1300  1A:1227-1300
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_BOXPS51698 U-box domain profile.UBE4B_HUMAN1227-1300  1A:1227-1300

(-) Exons   (0, 0)

(no "Exon" information available for 2KRE)

(-) 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:100
 aligned with UBE4B_HUMAN | O95155 from UniProtKB/Swiss-Prot  Length:1302

    Alignment length:103
                                  1209      1219      1229      1239      1249      1259      1269      1279      1289      1299   
         UBE4B_HUMAN   1200 AIEKFKLLAEKVEEIVAKNARAEIDYSDAPDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESMLEPVPELKEQIQAWMREKQNSDH 1302
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....---....................................eeee...eeeehhhhhhhh..................eehhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------U_BOX  PDB: A:1227-1300 UniProt: 1227-1300                                -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                2kre A 1203 GSHKF---AEKVEEIVAKNARAEIDYSDAPDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESMLEPVPELKEQIQAWMREKQNSDH 1302
                                | 1209      1219      1229      1239      1249      1259      1269      1279      1289      1299   
                             1207   |                                                                                              
                                 1208                                                                                              

   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 2KRE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (UBE4B_HUMAN | O95155)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0034450    ubiquitin-ubiquitin ligase activity    Isoenergetic transfer of ubiquitin from one protein to an existing ubiquitin chain via the reaction X-ubiquitin + Y-ubiquitin -> Y-ubiquitin-ubiquitin + X, where both the X-ubiquitin and Y-ubiquitin-ubiquitin linkages are thioester bonds between the C-terminal glycine of ubiquitin and a sulfhydryl side group of a cysteine residue.
biological process
    GO:0044257    cellular protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
    GO:0008626    granzyme-mediated apoptotic signaling pathway    A series of molecular signals induced by granzymes which triggers the apoptotic death of a cell. The pathway starts with reception of a granzyme signal, and ends when the execution phase of apoptosis is triggered. Granzymes are serine proteases that are secreted by cytotoxic T cells and natural killer cells to induce apoptosis in target cells.
    GO:0031175    neuron projection development    The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0043161    proteasome-mediated ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0051865    protein autoubiquitination    The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink.
    GO:0006513    protein monoubiquitination    Addition of a single ubiquitin group to a protein.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    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:0009411    response to UV    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 an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    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:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
    GO:0003222    ventricular trabecula myocardium morphogenesis    The process in which the anatomical structures of the trabecular cardiac ventricle muscle are generated and organized.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0000151    ubiquitin ligase complex    A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

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 Related Entries

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        UBE4B_HUMAN | O951553l1x 3l1z

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