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(-) Description

Title :  CRYSTAL STRUCTURE OF YERSINIA PESTIS YOPH IN COMPLEX WITH AN AMINOOXY-CONTAINING PLATFORM COMPOUND FOR INHIBITOR DESIGN
 
Authors :  G. T. Lountos, M. Bahta, B. Dyas, R. G. Ulrich, D. S. Waugh, T. R. Burke
Date :  14 Dec 10  (Deposition) - 16 Mar 11  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Protein Tyrosine Phosphatase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Bahta, G. T. Lountos, B. Dyas, S. Kim, R. G. Ulrich, D. S. Waugh, T. R. Burke
Utilization Of Nitrophenylphosphates And Oxime- Based Ligation For The Development Of Nanomolar Affinity Inhibitors Of The Yersinia Pestis Outer Protein H (Yoph) Phosphatase.
J. Med. Chem. V. 54 2933 2011
PubMed-ID: 21443195  |  Reference-DOI: 10.1021/JM200022G

(-) Compounds

Molecule 1 - PROTEIN-TYROSINE PHOSPHATASE YOPH
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PZZ1089
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PTPASE DOMAIN, RESIDUES 164-468
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Synonym: UNCHARACTERIZED PROTEIN YOPH, UNCHARACTERIZED PROTEIN YPCD1.67C

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1YI11Ligand/Ion[4-[3-(DIFLUORO-PHOSPHONO-METHYL)PHENYL]PHENYL]METHOXYAZANIUM

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:229 , ASP A:231 , ILE A:232 , ASP A:356 , GLN A:357 , CYS A:403 , ARG A:404 , ALA A:405 , GLY A:406 , VAL A:407 , GLY A:408 , ARG A:409 , GLN A:446 , HOH A:2274BINDING SITE FOR RESIDUE YI1 A1469

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y2F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y2F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y2F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y2F)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y2F)

(-) 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:282
 aligned with O68720_YERPE | O68720 from UniProtKB/TrEMBL  Length:468

    Alignment length:282
                                   196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466  
         O68720_YERPE   187 SPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCCRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVGDDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 468
               SCOP domains d2y2fa_ A: Protein-tyrosine phosphatase YopH, catalytic domain                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh.....................................eeeeee..eeeeee...hhhhhhhhhhhhhhh....eee..hhhhhhhhhhh........eee..eeeeeeeeeeeeee..eeeeeeeeeeee.....eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eee.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y2f A 187 SPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 468
                                   196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466
   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  (0, 0)

(no "CATH Domain" information available for 2Y2F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y2F)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O68720_YERPE | O68720)
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: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.

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 Related Entries

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

UniProtKB/TrEMBL
        O68720_YERPE | O68720: 1huf 1qz0 2ydu

(-) Related Entries Specified in the PDB File

1qz0 CRYSTAL STRUCTURE OF THE YERSINIA PESTIS PHOSPHATASE YOPHIN COMPLEX WITH A PHOSPHOTYROSYL MIMETIC-CONTAINING HEXAPEPTIDE