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(-) Description

Title :  CRYSTAL STRUCTURE OF YERSINIA PROTEIN TYROSINE PHOSPHATASE AT 2.5 ANGSTROMS AND THE COMPLEX WITH TUNGSTATE
 
Authors :  J. A. Stuckey, H. L. Schubert, E. B. Fauman, Z. -Y. Zhang, J. E. Dixon, M. A. Saper
Date :  16 Sep 94  (Deposition) - 20 Dec 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Protein Tyrosine Phosphatase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Stuckey, H. L. Schubert, E. B. Fauman, Z. Y. Zhang, J. E. Dixon, M. A. Saper
Crystal Structure Of Yersinia Protein Tyrosine Phosphatase At 2. 5 A And The Complex With Tungstate.
Nature V. 370 571 1994
PubMed-ID: 8052312  |  Reference-DOI: 10.1038/370571A0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN-TYROSINE PHOSPHATASE YERSINIA (CATALYTIC DOMAIN)
    Chains: A, B
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System Gene: YOP51
    Expression System Vector Type: PLASMID
    Gene: YOP51
    Organism Scientific: YERSINIA ENTEROCOLITICA
    Organism Taxid: 630

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1YPT)

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1APLAUTHORHIS A:402 , CYS 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
2BPLAUTHORHIS B:402 , CYS B:403 , ARG B:404 , ALA B:405 , GLY B:406 , VAL B:407 , GLY B:408 , ARG B:409 , THR B:410THE PHOSPHATE BINDING LOOP WHICH IS BELIEVED TO BE STRUCTURALLY CONSERVED IN ALL PROTEIN TYROSINE PHOSPHATASES
3WPDAUTHORHIS B:350 , VAL B:351 , GLY B:352 , ASN B:353 , TRP B:354 , PRO B:355 , ASP B:356 , GLN B:357 , THR B:358 , ALA B:359 , VAL B:360THE FLEXIBLE LOOP FROM MOLECULE B CONTAINING THE PUTATIVE GENERAL ACID, ASP 356, THAT FOLDS OVER THE ACTIVE SITE AND SEQUESTERS THE TUNGSTATE ANION IN THE TUNGSTATE-BOUND STRUCTURE.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.YOPH_YEREN366-451
 		  2A:366-451
B:366-451
2TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.YOPH_YEREN401-411
 		  2A:401-411
B:401-411

(-) Exons   (0, 0)

(no "Exon" information available for 1YPT)

(-) 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 d1ypta_ A: Protein-tyrosine phosphatase YopH, catalytic domain                                                                                                                                                                                                                         SCOP domains
               CATH domains 1yptA00 A:191-468 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.....................................eeeeee..eeeeee....hhhhhhhhhhhhh.....eee...hhhhh.hhh.........eee..eeeeeeeeeeee.....eeeeeeeeeee.....eeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhh...hhhh......eeee......hhhhhhhhhhhh.hhh....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
                 1ypt A 191 PEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 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        


Chain B from PDB  Type:PROTEIN  Length:280
 aligned with YOPH_YEREN | P15273 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:280
                                   198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468
           YOPH_YEREN   189 YGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCCRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 468
               SCOP domains d1yptb_ B: Protein-tyrosine phosphatase YopH, catalytic domain                                                                                                                                                                                                                           SCOP domains
               CATH domains 1yptB00 B:189-468 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) ----------------------------------Y_phosphatase-1yptB01 B:223-459                                                                                                                                                                                                              --------- Pfam domains (1)
           Pfam domains (2) ----------------------------------Y_phosphatase-1yptB02 B:223-459                                                                                                                                                                                                              --------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhh......................................eeeeee..eeeeee....hhhhhhhhhhhhh.....eee...hhhhh.hhh.........eee..eeeeeeeeeeee.....eeeeeeeeeee.....eeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhh..hhhh......eeee......hhhhhhhhhhh..hhh....hhhhhhhhhhh........hhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:366-451 UniProt: 366-451                                    ----------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA--------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ypt B 189 YGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 468
                                   198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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  1ypt
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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 1ytn 1yts 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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