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(-) Description

Title :  A LIGAND-INDUCED CONFORMATIONAL CHANGE IN THE YERSINIA PROTEIN TYROSINE PHOSPHATASE
 
Authors :  H. L. Schubert, J. A. Stuckey, E. B. Fauman, J. E. Dixon, M. A. Saper
Date :  07 Apr 95  (Deposition) - 10 Jul 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Tyrosine Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. L. Schubert, E. B. Fauman, J. A. Stuckey, J. E. Dixon, M. A. Saper
A Ligand-Induced Conformational Change In The Yersinia Protein Tyrosine Phosphatase.
Protein Sci. V. 4 1904 1995
PubMed-ID: 8528087
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - YERSINIA PROTEIN TYROSINE PHOSPHATASE
    Chains: A
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: YOP51
    Expression System Plasmid: PT7-7
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YOP51
    Mutation: YES
    Organism Scientific: YERSINIA ENTEROCOLITICA
    Organism Taxid: 630
    Strain: W22703

 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
1SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:356 , SER A:403 , ARG A:404 , ALA A:405 , GLY A:406 , VAL A:407 , GLY A:408 , ARG A:409 , HOH A:522BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWAREARG A:278 , SER A:388 , SER A:389 , ALA A:390BINDING SITE FOR RESIDUE SO4 A 2
3PLAUTHORHIS A:402 , SER A:403 , ARG A:404 , ALA A:405 , GLY A:406 , VAL A:407 , GLY A:408 , ARG A:409 , THR A:410THE PHOSPHATE BINDING LOOP WHICH IS BELIEVED TO BE STRUCTURALLY CONSERVED IN ALL PROTEIN TYROSINE PHOSPHATASES
4WPDAUTHORHIS A:350 , VAL A:351 , GLY A:352 , ASN A:353 , TRP A:354 , PRO A:355 , ASP A:356 , GLN A:357 , THR A:358 , ALA A:359 , VAL A:360THE FLEXIBLE LOOP CONTAINING THE PUTATIVE GENERAL ACID, ASP 356, THAT FOLDS OVER THE SULFATE ANION IN THE SULFATE-BOUND STRUCTURE.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YTS)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.YOPH_YEREN366-451  1A:366-451
2TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.YOPH_YEREN401-411  1A:401-411

(-) Exons   (0, 0)

(no "Exon" information available for 1YTS)

(-) 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:278
 aligned with YOPH_YEREN | P15273 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:278
                                   200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460        
           YOPH_YEREN   191 PEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCCRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 468
               SCOP domains d1ytsa_ A: Protein-tyrosine phosphatase YopH, catalytic domain                                                                                                                                                                                                                         SCOP domains
               CATH domains 1ytsA00 A:191-468 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------Y_phosphatase-1ytsA01 A:223-459                                                                                                                                                                                                              --------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh............................hhh.......eeeeee..eeeeee....hhhhhhhhhhhhh.....eee...hhhhh.hhh.........eee..eeeeeee..eeeee..eeeeeeeeeeee.....eeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhh...hhh......eeee......hhhhhhhhhhhh........hhhhhhhhhhh........hhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:366-451 UniProt: 366-451                                    ----------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA--------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yts A 191 PEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHSRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 468
                                   200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Phosphatase (121)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YOPH_YEREN | P15273)
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: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.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        YOPH_YEREN | P15273: 1lyv 1pa9 1xxp 1xxv 1ypt 1ytn 1ytw 2i42 3blt 3blu 3bm8 3f99 3f9a 3f9b 3u96 4gf3 4yaa 4z6b 4zi4 4zn5

(-) Related Entries Specified in the PDB File

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