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(-) Description

Title :  CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF DUAL SPECIFICITY PHOSPHATASE 26, MS0830 FROM HOMO SAPIENS
 
Authors :  Y. Xie, S. Kishishita, K. Murayama, C. Hori-Takemoto, L. Chen, Z. J. Liu B. C. Wang, M. Shirozu, S. Yokoyama, Riken Structural Genomics/Pro Initiative (Rsgi)
Date :  13 Oct 06  (Deposition) - 16 Oct 07  (Release) - 12 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Conserved Hypothetical Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Y. Won, Y. Xie, C. Takemoto, L. Chen, Z. J. Liu, B. C. Wang, D. Lee, E. J. Woo, S. G. Park, M. Shirouzu, S. Yokoyama, S. J. Kim, S. W. Chi
High-Resolution Crystal Structure Of The Catalytic Domain O Human Dual-Specificity Phosphatase 26.
Acta Crystallogr. , Sect. D V. 69 1160 2013
PubMed-ID: 23695260  |  Reference-DOI: 10.1107/S0907444913004770

(-) Compounds

Molecule 1 - DUAL SPECIFICITY PHOSPHATASE 26
    ChainsA
    EC Number3.1.3.48
    EngineeredYES
    Expression System PlasmidPK060110-18-MD01
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN, RESIDUES 61-211
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymMS0830, PUTATIVE, LOW-MOLECULAR-MASS DUAL- SPECIFICITY PHOSPHATASE 4, DUAL-SPECIFICITY PHOSPHATASE SKRP3, MITOGEN-ACTIVATED PROTEIN KINASE PHOSPHATASE 8, NATA1 PROTEIN, CDNA FLJ31142 FIS, CLONE IMR322001317, WEAKLY SIMILAR TO HOMO SAPIENS PROTEIN PHOSPHATASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2E0T)

(-) Sites  (0, 0)

(no "Site" information available for 2E0T)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E0T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2E0T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E0T)

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_DUALPS50054 Dual specificity protein phosphatase family profile.DUS26_HUMAN61-206  1A:61-206
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.DUS26_HUMAN128-186  1A:128-186
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.DUS26_HUMAN150-160  1A:150-160
Biological Unit 1 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_DUALPS50054 Dual specificity protein phosphatase family profile.DUS26_HUMAN61-206  2A:61-206
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.DUS26_HUMAN128-186  2A:128-186
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.DUS26_HUMAN150-160  2A:150-160

(-) Exons   (3, 3)

Asymmetric Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002562611aENSE00002123562chr8:33457624-33457183442DUS26_HUMAN-00--
1.2cENST000002562612cENSE00000911631chr8:33455109-33454813297DUS26_HUMAN1-74741A:61-7414
1.3aENST000002562613aENSE00000911629chr8:33451265-33451051215DUS26_HUMAN74-146731A:74-14673
1.4bENST000002562614bENSE00000980064chr8:33449730-33448856875DUS26_HUMAN146-211661A:146-21065

(-) 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:150
 aligned with DUS26_HUMAN | Q9BV47 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:150
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
          DUS26_HUMAN    61 HADEVWPGLYLGDQDMANNRRELRRLGITHVLNASHSRWRGTPEAYEGLGIRYLGVEAHDSPAFDMSIHFQTAADFIHRALSQPGGKILVHCAVGVSRSATLVLAYLMLYHHLTLVEAIKKVKDHRGIIPNRGFLRQLLALDRRLRQGLE 210
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eeeehhhhhhhhhhhhhhh..eeee...........hhhhhh.eeee..........hhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) TYR_PHOSPHATASE_DUAL  PDB: A:61-206 UniProt: 61-206                                                                                               ---- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:128-186 UniProt: 128-186         ------------------------ PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------TYR_PHOSPHA-------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.2c     -----------------------------------------------------------------------Exon 1.4b  PDB: A:146-210 UniProt: 146-211 [INCOMPLETE]           Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.3a  PDB: A:74-146 UniProt: 74-146                                 ---------------------------------------------------------------- Transcript 1 (2)
                 2e0t A  61 HADEVWPGLYLGDQDMANNRRELRRLGITHVLNASHSRWRGTPEAYEGLGIRYLGVEAHDSPAFDMSIHFQTAADFIHRALSQPGGKILVHCAVGVSRSATLVLAYLMLYHHLTLVEAIKKVKDHRGIIPNRGFLRQLLALDRRLRQGLE 210
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

   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 2E0T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2E0T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E0T)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A   (DUS26_HUMAN | Q9BV47)
molecular function
    GO:0001102    RNA polymerase II activating transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
    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:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    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:0004647    phosphoserine phosphatase activity    Catalysis of the reaction: L(or D)-O-phosphoserine + H2O = L(or D)-serine + phosphate.
    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: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:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    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: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:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0045785    positive regulation of cell adhesion    Any process that activates or increases the frequency, rate or extent of cell adhesion.
    GO:1902310    positive regulation of peptidyl-serine dephosphorylation    Any process that activates or increases the frequency, rate or extent of peptidyl-serine dephosphorylation.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
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: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:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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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        DUS26_HUMAN | Q9BV474b04 4hrf 5gtj

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