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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MUD1 UBA DOMAIN
 
Authors :  J. -F. Trempe, N. R. Brown, E. D. Lowe, M. E. M. Noble, C. Gordon, I. D. Campbell, L. N. Johnson, J. A. Endicott
Date :  31 Mar 05  (Deposition) - 04 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Uba, Ubiquitin, Three-Helix Bundle, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. -F. Trempe, N. R. Brown, E. D. Lowe, C. Gordon, I. D. Campbell, M. E. M. Noble, J. A. Endicott
Mechanism Of Lys48-Linked Polyubiquitin Chain Recognition By The Mud1 Uba Domain
Embo J. V. 24 3178 2005
PubMed-ID: 16138082  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600797
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBA-DOMAIN PROTEIN MUD1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-6P1
    Expression System StrainBL21 DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL UBA
    GeneMUD1
    Organism CommonFISSION YEAST
    Organism ScientificSCHIZOSACCHAROMYCES POMBE
    Organism Taxid4896
    SynonymUBA-DOMAIN CONTAINING PROTEIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1Z96)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z96)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z96)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z96)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z96)

(-) Sequences/Alignments

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   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:38
 aligned with MUD1_SCHPO | Q10256 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:38
                                   304       314       324        
           MUD1_SCHPO   295 GLNSKIAQLVSMGFDPLEAAQALDAANGDLDVAASFLL 332
               SCOP domains d1z96a1 A:295-332                      SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 1z96 A 295 GLNSKIAQLVSMGFDPLEAAQALDAANGDLDVAASFLL 332
                                   304       314       324        

Chain B from PDB  Type:PROTEIN  Length:35
 aligned with MUD1_SCHPO | Q10256 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:35
                                   307       317       327     
           MUD1_SCHPO   298 SKIAQLVSMGFDPLEAAQALDAANGDLDVAASFLL 332
               SCOP domains d1z96b_ B: UBA-domain protein mud1  SCOP domains
               CATH domains ----------------------------------- CATH domains
           Pfam domains (1) UBA-1z96B01 B:298-331             - Pfam domains (1)
           Pfam domains (2) UBA-1z96B02 B:298-331             - Pfam domains (2)
         Sec.struct. author hhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                 1z96 B 298 SKIAQLVSMGFDPLEAAQALDAANGDLDVAASFLL 332
                                   307       317       327     

   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Z96)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: UBA (32)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MUD1_SCHPO | Q10256)
molecular function
    GO:0000149    SNARE binding    Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein.
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0031593    polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination of the target protein.
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
    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: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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0017157    regulation of exocytosis    Any process that modulates the frequency, rate or extent of exocytosis.
    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: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.
cellular component
    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.

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