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(-) Description

Title :  PTYR BOUND FORM OF SDP-1
 
Authors :  D. C. Briggs, N. Q. Mcdonald
Date :  09 Aug 06  (Deposition) - 22 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.84
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Protein Phosphatase, Hypothetical Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. C. Fox, M. Shafiq, D. C. Briggs, P. P. Knowles, M. Collister, M. J. Didmon, V. Makrantoni, R. J. Dickinson, S. Hanrahan, N. Totty, M. J. R. Stark, S. M. Keyse, N. Q. Mcdonald
Redox-Mediated Substrate Recognition By Sdp1 Defines A New Group Of Tyrosine Phosphatases
Nature V. 447 487 2007
PubMed-ID: 17495930  |  Reference-DOI: 10.1038/NATURE05804

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE YIL113W
    ChainsA, B
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET14B
    Expression System StrainFB810
    Expression System Taxid562
    Expression System VariantPLYSS
    FragmentRESIDUES 17-198
    MutationYES
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    StrainS288C / AB972
    SynonymSDP-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  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1MG5Ligand/IonMAGNESIUM ION
2PTR2Ligand/IonO-PHOSPHOTYROSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PTR1Ligand/IonO-PHOSPHOTYROSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PTR1Ligand/IonO-PHOSPHOTYROSINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:73 , ASN A:93BINDING SITE FOR RESIDUE MG A1197
2AC2SOFTWAREGLU A:110 , ASP A:112 , HOH A:2009BINDING SITE FOR RESIDUE MG A1198
3AC3SOFTWAREGLU B:73 , ASN B:93BINDING SITE FOR RESIDUE MG B1197
4AC4SOFTWAREGLU B:134 , HOH B:2005BINDING SITE FOR RESIDUE MG B1198
5AC5SOFTWAREVAL B:99 , PRO B:100 , VAL B:102BINDING SITE FOR RESIDUE MG B1199
6AC6SOFTWAREHIS A:111 , SER A:140 , GLN A:141 , CYS A:142 , GLY A:143 , LEU A:144 , SER A:145 , ARG A:146BINDING SITE FOR RESIDUE PTR A1199
7AC7SOFTWAREHIS B:111 , SER B:140 , GLN B:141 , CYS B:142 , GLY B:143 , LEU B:144 , SER B:145 , ARG B:146BINDING SITE FOR RESIDUE PTR B1200

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:47 -A:142
2B:47 -B:142

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J17)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J17)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_DUALPS50054 Dual specificity protein phosphatase family profile.SDP1_YEAST72-195
 
  2A:72-195
B:72-195
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.SDP1_YEAST117-173
 
  2A:117-173
B:117-173
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.SDP1_YEAST138-148
 
  2A:138-148
B:138-148
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_DUALPS50054 Dual specificity protein phosphatase family profile.SDP1_YEAST72-195
 
  1A:72-195
-
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.SDP1_YEAST117-173
 
  1A:117-173
-
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.SDP1_YEAST138-148
 
  1A:138-148
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_DUALPS50054 Dual specificity protein phosphatase family profile.SDP1_YEAST72-195
 
  1-
B:72-195
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.SDP1_YEAST117-173
 
  1-
B:117-173
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.SDP1_YEAST138-148
 
  1-
B:138-148

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YIL113W1YIL113W.1IX:150556-151185630SDP1_YEAST1-2092092A:47-197 (gaps)
B:47-197 (gaps)
151
151

(-) 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:145
 aligned with SDP1_YEAST | P40479 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:151
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196 
           SDP1_YEAST    47 CSSLDVRRIYPKGPLLVLPEKIYLYSEPTVKELLPFDVVINVAEEANDLRMQVPAVEYHHYRWEHDSQIALDLPSLTSIIHAATTKREKILIHCQCGLSRSATLIIAYIMKYHNLSLRHSYDLLKSRADKINPSIGLIFQLMEWEVALNAK 197
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .------.......eeee...eeee....hhhhh...eeee...............eeee.......hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------TYR_PHOSPHATASE_DUAL  PDB: A:72-195 UniProt: 72-195                                                                         -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:117-173 UniProt: 117-173       ------------------------ PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------- PROSITE (3)
               Transcript 1 Exon 1.1  PDB: A:47-197 (gaps) UniProt: 1-209 [INCOMPLETE]                                                                                              Transcript 1
                 2j17 A  47 C------RIYPKGPLLVLPEKIYLYSEPTVKELLPFDVVINVAEEANDLRMQVPAVEYHHYRWEHDSQIALDLPSLTSIIHAATTKREKILIHSQCGLSRSATLIIAYIMKYHNLSLRHSYDLLKSRADKINPSIGLIFQLMEWEVALNAK 197
                            |      |56        66        76        86        96       106       116       126       136       146       156       166       176       186       196 
                            |     54                                                                                                                                               
                           47                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with SDP1_YEAST | P40479 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:151
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196 
           SDP1_YEAST    47 CSSLDVRRIYPKGPLLVLPEKIYLYSEPTVKELLPFDVVINVAEEANDLRMQVPAVEYHHYRWEHDSQIALDLPSLTSIIHAATTKREKILIHCQCGLSRSATLIIAYIMKYHNLSLRHSYDLLKSRADKINPSIGLIFQLMEWEVALNAK 197
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-----........eeee...eeee....hhhhh...eeee...............eeee.......hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh..hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------TYR_PHOSPHATASE_DUAL  PDB: B:72-195 UniProt: 72-195                                                                         -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:117-173 UniProt: 117-173       ------------------------ PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------- PROSITE (3)
               Transcript 1 Exon 1.1  PDB: B:47-197 (gaps) UniProt: 1-209 [INCOMPLETE]                                                                                              Transcript 1
                 2j17 B  47 C-----RRIYPKGPLLVLPEKIYLYSEPTVKELLPFDVVINVAEEANDLRMQVPAVEYHHYRWEHDSQIALDLPSLTSIIHAATTKREKILIHSQCGLSRSATLIIAYIMKYHNLSLRHSYDLLKSRADKINPSIGLIFQLMEWEVALNAK 197
                            |     | 56        66        76        86        96       106       116       126       136       146       156       166       176       186       196 
                           47    53                                                                                                                                                

   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 2J17)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J17)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J17)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SDP1_YEAST | P40479)
molecular function
    GO:0033550    MAP kinase tyrosine phosphatase activity    Catalysis of the reaction: MAP kinase tyrosine phosphate + H2O = MAP kinase tyrosine + 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:0000196    MAPK cascade involved in cell wall organization or biogenesis    A MAPK cascade that contributes to cell wall organization or biogenesis.
    GO:0000754    adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion    In organisms that undergo conjugation with cellular fusion, the process resulting in desensitization following exposure to pheromone stimulus that act to down-regulate further stimulation or block initial conjugation responses. An example of this is the adaptation to pheromone during conjugation with cellular fusion in Saccharomyces cerevisiae.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0000200    inactivation of MAPK activity involved in cell wall organization or biogenesis    Any process that terminates the activity of the active enzyme MAP kinase in the context of cell wall organization or biogenesis.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:1990264    peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity    Any peptidyl-tyrosine dephosphorylation that is involved in inactivation of protein kinase activity.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0010969    regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion    Any process that modulates the frequency, rate or extent of pheromone-dependent signal transduction during conjugation with cellular fusion, a signal transduction process resulting in the relay, amplification or dampening of a signal generated in response to pheromone exposure in organisms that undergo conjugation with cellular fusion.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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
        SDP1_YEAST | P404792j16

(-) Related Entries Specified in the PDB File

2j16 APO & SULPHATE BOUND FORMS OF SDP-1