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(-) Description

Title :  CRYSTAL STRUCTURE OF PYST1 (MKP3)
 
Authors :  A. E. Stewart, S. Dowd, S. Keyse, N. Q. Mcdonald
Date :  11 Jul 98  (Deposition) - 22 Jul 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. E. Stewart, S. Dowd, S. M. Keyse, N. Q. Mcdonald
Crystal Structure Of The Mapk Phosphatase Pyst1 Catalytic Domain And Implications For Regulated Activation.
Nat. Struct. Biol. V. 6 174 1999
PubMed-ID: 10048930  |  Reference-DOI: 10.1038/5861
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYST1
    ChainsA
    EC Number3.1.3.48, 3.1.3.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET14B
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    FragmentCATALYTIC DOMAIN
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsMPD AND CHLORIDE ION
    SynonymDUAL SPECIFICITY PHOSPHATASE, MAP KINASE PHOSPHATASE 3, MKP-3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:293 , ARG A:299BINDING SITE FOR RESIDUE CL A 500
2AC2SOFTWAREMET A:316 , ASN A:317 , TYR A:320 , ASN A:333 , PHE A:336 , LEU A:340 , HOH A:404BINDING SITE FOR RESIDUE MPD A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MKP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051751N313IDUS6_HUMANPolymorphism12828557AN313I
2UniProtVAR_069946T346MDUS6_HUMANDisease (HH19)146089505AT346M

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_DUALPS50054 Dual specificity protein phosphatase family profile.DUS6_HUMAN206-348  1A:206-347
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.DUS6_HUMAN262-330  1A:262-330

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002794881ENSE00001214153chr12:89746296-89745417880DUS6_HUMAN1-1341340--
1.2ENST000002794882ENSE00001096871chr12:89744802-89744365438DUS6_HUMAN134-2801471A:204-28077
1.3ENST000002794883ENSE00001186650chr12:89743338-897418391500DUS6_HUMAN280-3811021A:280-34768

(-) 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    
   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:144
 aligned with DUS6_HUMAN | Q16828 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:144
                                   213       223       233       243       253       263       273       283       293       303       313       323       333       343    
           DUS6_HUMAN   204 PSFPVEILPFLYLGCAKDSTNLDVLEEFGIKYILNVTPNLPNLFENAGEFKYKQIPISDHWSQNLSQFFPEAISFIDEARGKNCGVLVHCLAGISRSVTVTVAYLMQKLNLSMNDAYDIVKMKKSNISPNFNFMGQLLDFERTL 347
               SCOP domains d1mkpa_ A: Mapk phosphatase                                                                                                                      SCOP domains
               CATH domains 1mkpA00 A:204-347 Protein tyrosine phosphatase superfamily                                                                                       CATH domains
               Pfam domains ----------DSPc-1mkpA01 A:214-346                                                                                                               - Pfam domains
         Sec.struct. author ....eeee..eeee.......hhhhhh..eeeeee.......eeeee..eeeee...........hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhh....hhhhhhhhhhh..........hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------I--------------------------------M- SAPs(SNPs)
                PROSITE (1) --TYR_PHOSPHATASE_DUAL  PDB: A:206-347 UniProt: 206-348                                                                                          PROSITE (1)
                PROSITE (2) ----------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:262-330 UniProt: 262-330                   ----------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:204-280 UniProt: 134-280 [INCOMPLETE]                       ------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------Exon 1.3  PDB: A:280-347 UniProt: 280-381 [INCOMPLETE]               Transcript 1 (2)
                 1mkp A 204 ASFPVEILPFLYLGCAKDSTNLDVLEEFGIKYILNVTPNLPNLFENAGEFKYKQIPISDHWSQNLSQFFPEAISFIDEARGKNCGVLVHSLAGISRSVTVTVAYLMQKLNLSMNDAYDIVKMKKSNISPNFNFMGQLLDFERTL 347
                                   213       223       233       243       253       263       273       283       293       303       313       323       333       343    

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DUS6_HUMAN | Q16828)
molecular function
    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:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and 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:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0009953    dorsal/ventral pattern formation    The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
    GO:0000188    inactivation of MAPK activity    Any process that terminates the activity of the active enzyme MAP kinase.
    GO:0070373    negative regulation of ERK1 and ERK2 cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0010942    positive regulation of cell death    Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0042663    regulation of endodermal cell fate specification    Any process that mediates the specification of a cell into an endoderm cell.
    GO:0040036    regulation of fibroblast growth factor receptor signaling pathway    Any process that modulates the frequency, rate or extent of fibroblast growth factor receptor signaling pathway activity.
    GO:0060420    regulation of heart growth    Any process that modulates the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart.
    GO:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0070848    response to growth factor    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 growth factor stimulus.
    GO:0051409    response to nitrosative 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 nitrosative stress stimulus. Nitrosative stress is a state often resulting from exposure to high levels of nitric oxide (NO) or the highly reactive oxidant peroxynitrite, which is produced following interaction of NO with superoxide anions.
    GO:0014070    response to organic cyclic compound    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 cyclic compound stimulus.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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        DUS6_HUMAN | Q168281hzm

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