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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MAP KINASE BINDING DOMAIN OF MKP5
 
Authors :  X. Tao, L. Tong
Date :  10 Feb 07  (Deposition) - 07 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rhodanese Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Tao, L. Tong
Crystal Structure Of The Map Kinase Binding Domain And The Catalytic Domain Of Human Mkp5.
Protein Sci. V. 16 880 2007
PubMed-ID: 17400920  |  Reference-DOI: 10.1110/PS.062712807
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DUAL SPECIFICITY PROTEIN PHOSPHATASE 10
    ChainsA, B
    EC Number3.1.3.48, 3.1.3.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRHODANESE DOMAIN (RESIDUES 148-287)
    GeneMKP5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMITOGEN-ACTIVATED PROTEIN KINASE PHOSPHATASE 5, MAP KINASE PHOSPHATASE 5, MKP-5

 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 2OUC)

(-) Sites  (0, 0)

(no "Site" information available for 2OUC)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RHODANESE_3PS50206 Rhodanese domain profile.DUS10_HUMAN168-285
 
  2A:172-285
B:172-285
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RHODANESE_3PS50206 Rhodanese domain profile.DUS10_HUMAN168-285
 
  1A:172-285
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RHODANESE_3PS50206 Rhodanese domain profile.DUS10_HUMAN168-285
 
  1-
B:172-285

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003668991aENSE00001900138chr1:221915518-221915323196DUS10_HUMAN-00--
1.2aENST000003668992aENSE00002151685chr1:221913129-221912276854DUS10_HUMAN1-2712712A:148-271 (gaps)
B:148-271 (gaps)
124
124
1.5ENST000003668995ENSE00001745171chr1:221879808-221879437372DUS10_HUMAN271-3951252A:271-289
B:271-289
19
19
1.6dENST000003668996dENSE00001285025chr1:221876019-2218747661254DUS10_HUMAN395-482880--

(-) Sequences/Alignments

Asymmetric 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:132
 aligned with DUS10_HUMAN | Q9Y6W6 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:142
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287  
          DUS10_HUMAN   148 KIIYPNDLAKKMTKCSKSHLPSQGPVIIDCRPFMEYNKSHIQGAVHINCADKISRRRLQQGKITVLDLISCREGKDSFKRIFSKEIIVYDENTNEPSRVMPSQPLHIVLESLKREGKEPLVLKGGLSSFKQNHENLCDNSLQ 289
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhh----------.eeee..hhhhhhheee...ee....hhhhhhhhhh...hhhhhhhh....hhhhhhhhh.eeee.....hhhhh...hhhhhhhhhhhhh....eee.hhhhhhhhhhhh.eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------RHODANESE_3  PDB: A:172-285 UniProt: 168-285                                                                          ---- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:148-271 (gaps) UniProt: 1-271 [INCOMPLETE]                                                                ------------------ Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------Exon 1.5            Transcript 1 (2)
                 2ouc A 148 KIIYPNDLAKKMTK----------PVIIDCRPFMEYNKSHIQGAVHINCADKISRRRLQQGKITVLDLISCREGKDSFKRIFSKEIIVYDENTNEPSRVMPSQPLHIVLESLKREGKEPLVLKGGLSSFKQNHENLCDNSKE 289
                                   157   |     -    |  177       187       197       207       217       227       237       247       257       267       277       287  
                                       161        172                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:132
 aligned with DUS10_HUMAN | Q9Y6W6 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:142
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287  
          DUS10_HUMAN   148 KIIYPNDLAKKMTKCSKSHLPSQGPVIIDCRPFMEYNKSHIQGAVHINCADKISRRRLQQGKITVLDLISCREGKDSFKRIFSKEIIVYDENTNEPSRVMPSQPLHIVLESLKREGKEPLVLKGGLSSFKQNHENLCDNSLQ 289
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhh.----------.eeee..hhhhhhheee...ee....hhhhhhhhhh...hhhhhhhh....hhhhhhh...eeee.....hhhhh...hhhhhhhhhhhhh....eee.hhhhhhhhhhh..eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------RHODANESE_3  PDB: B:172-285 UniProt: 168-285                                                                          ---- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:148-271 (gaps) UniProt: 1-271 [INCOMPLETE]                                                                ------------------ Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------Exon 1.5            Transcript 1 (2)
                 2ouc B 148 KIIYPNDLAKKMTK----------PVIIDCRPFMEYNKSHIQGAVHINCADKISRRRLQQGKITVLDLISCREGKDSFKRIFSKEIIVYDENTNEPSRVMPSQPLHIVLESLKREGKEPLVLKGGLSSFKQNHENLCDNSKE 289
                                   157   |     -    |  177       187       197       207       217       227       237       247       257       267       277       287  
                                       161        172                                                                                                                     

   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 2OUC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DUS10_HUMAN | Q9Y6W6)
molecular function
    GO:0033549    MAP kinase phosphatase activity    Catalysis of the reaction: a phosphorylated MAP kinase + H2O = a MAP kinase + phosphate.
    GO:0017017    MAP kinase tyrosine/serine/threonine phosphatase activity    Catalysis of the reaction: MAP kinase serine/threonine/tyrosine phosphate + H2O = MAP kinase serine/threonine/tyrosine + phosphate.
    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:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0008138    protein tyrosine/serine/threonine phosphatase activity    Catalysis of the reactions: protein serine + H2O = protein serine + phosphate; protein threonine phosphate + H2O = protein threonine + phosphate; and protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    GO:0007254    JNK cascade    An intracellular protein kinase cascade containing at least a JNK (a MAPK), a JNKK (a MAPKK) and a JUN3K (a MAP3K). The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0000188    inactivation of MAPK activity    Any process that terminates the activity of the active enzyme MAP kinase.
    GO:0046329    negative regulation of JNK cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the JNK cascade.
    GO:0043508    negative regulation of JUN kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of JUN kinase activity.
    GO:0048715    negative regulation of oligodendrocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of oligodendrocyte differentiation.
    GO:0044387    negative regulation of protein kinase activity by regulation of protein phosphorylation    The stopping, prevention, or reduction in frequency, rate or extent of protein kinase activity as a result of regulating the phosphorylation status of that protein kinase.
    GO:0060266    negative regulation of respiratory burst involved in inflammatory response    Any process that decreases the rate, frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases made as a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.
    GO:0032873    negative regulation of stress-activated MAPK cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the stress-activated MAPK cascade.
    GO:0048709    oligodendrocyte differentiation    The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0002819    regulation of adaptive immune response    Any process that modulates the frequency, rate, or extent of an adaptive immune response.
    GO:0090335    regulation of brown fat cell differentiation    Any process that modulates the rate, frequency, or extent of brown fat cell differentiation. Brown fat cell differentiation is the process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.
    GO:0045088    regulation of innate immune response    Any process that modulates the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0010033    response to organic substance    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 organic substance stimulus.
    GO:0006950    response to stress    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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DUS10_HUMAN | Q9Y6W61zzw 2oud 3tg1

(-) Related Entries Specified in the PDB File

2oud