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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A E280A MUTANT OF THE CATALYTIC DOMAIN OF AMSH
 
Authors :  C. W. Davies, C. Das
Date :  12 May 11  (Deposition) - 19 Oct 11  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym./Biol. Unit :  A
Keywords :  Ubiquitin Hydrolase, Stam, Endosome-Associated Deubiquitinating Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. W. Davies, L. N. Paul, M. I. Kim, C. Das
Structural And Thermodynamic Comparison Of The Catalytic Domain Of Amsh And Amsh-Lp: Nearly Identical Fold But Different Stability.
J. Mol. Biol. V. 413 416 2011
PubMed-ID: 21888914  |  Reference-DOI: 10.1016/J.JMB.2011.08.029

(-) Compounds

Molecule 1 - STAM-BINDING PROTEIN
    ChainsA
    EC Number3.4.19.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P1
    Expression System StrainROSETTA
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN, RESIDUES 219-424
    GeneAMSH, STAMBP, STAMBP (AMSH)
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM, ENDOSOME- ASSOCIATED UBIQUITIN ISOPEPTIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:309 , HIS A:335 , HIS A:337 , ASP A:348BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWAREHIS A:350 , CYS A:390 , HIS A:396 , HIS A:398BINDING SITE FOR RESIDUE ZN A 2

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:282 -A:311

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:401 -Pro A:402

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069811T313ISTABP_HUMANDisease (MICCAP)202100019AT313I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RZV)

(-) Exons   (0, 0)

(no "Exon" information available for 3RZV)

(-) 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    
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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:179
 aligned with STABP_HUMAN | O95630 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:179
                                   255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415         
          STABP_HUMAN   246 ESIPTIDGLRHVVVPGRLCPQFLQLASANTARGVETCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCSPKFQETGFFKLTDHGLEEISSCRQKGFHPHSKDPPLFCSCSHVTVVDRAVTITDLR 424
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee.hhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee..eee....eee.hhhhhhhhhhhhh.eeeeeeee........hhhhhhhhhhhhhhh...eeeeee....eeeeeeehhhhhhhhhhh..............eee...eeee....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------I--------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rzv A 246 ESIPTIDGLRHVVVPGRLCPQFLQLASANTARGVATCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCSPKFQETGFFKLTDHGLEEISSCRQKGFHPHSKDPPLFCSCSHVTVVDRAVTITDLR 424
                                   255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415         

   Legend:   → Mismatch (orange background)
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  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 3RZV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RZV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RZV)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (STABP_HUMAN | O95630)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0004843    thiol-dependent ubiquitin-specific protease activity    Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein.
biological process
    GO:0007259    JAK-STAT cascade    Any process in which STAT proteins (Signal Transducers and Activators of Transcription) and JAK (Janus Activated Kinase) proteins convey a signal to trigger a change in the activity or state of a cell. The JAK-STAT cascade begins with activation of STAT proteins by members of the JAK family of tyrosine kinases, proceeds through dimerization and subsequent nuclear translocation of STAT proteins, and ends with regulation of target gene expression by STAT proteins.
    GO:0000281    mitotic cytokinesis    A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells.
    GO:0046580    negative regulation of Ras protein signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of Ras protein signal transduction.
    GO:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:0014067    negative regulation of phosphatidylinositol 3-kinase signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0016579    protein deubiquitination    The removal of one or more ubiquitin groups from a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0032154    cleavage furrow    The cleavage furrow is a plasma membrane invagination at the cell division site. The cleavage furrow begins as a shallow groove and eventually deepens to divide the cytoplasm.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        STABP_HUMAN | O956302xze 3rzu 5ixf

(-) Related Entries Specified in the PDB File

2znr HOMOLOGOUS PROTEIN WITH AN ACTIVE SITE MUTATION.
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