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(-) Description

Title :  CRYSTAL STRUCTURE OF YOPHQ357F(CATALYTIC DOMAIN, RESIDUES 163-468) IN COMPLEX WITH PNCS
 
Authors :  M. C. Ho, S. Ke
Date :  17 Oct 11  (Deposition) - 29 Aug 12  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Yoph, Ptpase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Ke, M. C. Ho, N. Zhadin, H. Deng, R. Callender
Investigation Of Catalytic Loop Structure, Dynamics, And Function Relationship Of Yersinia Protein Tyrosine Phosphatase By Temperature-Jump Relaxation Spectroscopy And X-Ray Structural Determination.
J. Phys. Chem. B V. 116 6166 2012
PubMed-ID: 22564106  |  Reference-DOI: 10.1021/JP3037846

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE YOPH
    ChainsA, B
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPT7-7
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 163-468
    GeneYOP51, YOPH
    MutationYES
    Organism ScientificYERSINIA ENTEROCOLITICA
    Organism Taxid630
    SynonymVIRULENCE PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (1x)A 
Biological Unit 3 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CSN2Ligand/IonN,4-DIHYDROXY-N-OXO-3-(SULFOOXY)BENZENAMINIUM
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CSN2Ligand/IonN,4-DIHYDROXY-N-OXO-3-(SULFOOXY)BENZENAMINIUM
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CSN1Ligand/IonN,4-DIHYDROXY-N-OXO-3-(SULFOOXY)BENZENAMINIUM
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1CSN1Ligand/IonN,4-DIHYDROXY-N-OXO-3-(SULFOOXY)BENZENAMINIUM
2SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:229 , 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:481 , HOH A:483BINDING SITE FOR RESIDUE CSN A 1
2AC2SOFTWAREARG A:278 , LYS A:342 , SER A:388 , SER A:389 , HOH A:513BINDING SITE FOR RESIDUE SO4 A 469
3AC3SOFTWAREPHE A:357 , HOH B:72 , PHE B:229 , ILE B:232 , ASP B:356 , PHE B:357 , CYS B:403 , ARG B:404 , ALA B:405 , GLY B:406 , VAL B:407 , GLY B:408 , ARG B:409 , GLN B:446BINDING SITE FOR RESIDUE CSN B 1
4AC4SOFTWAREARG B:278 , LYS B:342 , SER B:388 , SER B:389 , ALA B:390BINDING SITE FOR RESIDUE SO4 B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U96)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Cys A:221 -Gly A:222
2Gly A:222 -Gly A:223
3Gly B:222 -Gly B:223

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U96)

(-) PROSITE Motifs  (2, 4)

Asymmetric 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
Biological Unit 1 (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
Biological Unit 2 (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
-
Biological Unit 3 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.YOPH_YEREN366-451
 
  1-
B:366-451
2TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.YOPH_YEREN401-411
 
  1-
B:401-411

(-) Exons   (0, 0)

(no "Exon" information available for 3U96)

(-) 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:282
 aligned with YOPH_YEREN | P15273 from UniProtKB/Swiss-Prot  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  
           YOPH_YEREN   187 SPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCCRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 468
               SCOP domains d3u96a_ A: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh.........................hhhhh......eeeeee..eeeeee...hhhhhhhhhhhhhhh....eee..hhhhhhhhhhh........eee..eeeeeeeeeeeeee..eeeeeeeeeeee.....eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eee.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhhh....... 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
                 3u96 A 187 SPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDFTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 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  

Chain B from PDB  Type:PROTEIN  Length:282
 aligned with YOPH_YEREN | P15273 from UniProtKB/Swiss-Prot  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  
           YOPH_YEREN   187 SPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCCRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 468
               SCOP domains d3u96b_ B: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh..........................hhhhh......eeeeee..eeeeee...hhhhhhhhhhhhhhh....eee..hhhhhhhhhhh........eee..eeeeeeeeeeeeee..eeeeeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eee.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhhh....... 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
                 3u96 B 187 SPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDFTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 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)
    → 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 Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U96)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U96)

(-) Gene Ontology  (9, 9)

Asymmetric 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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  3u96
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  3.1.3.48
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 Related Entries

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

UniProtKB/Swiss-Prot
        YOPH_YEREN | P152731lyv 1pa9 1xxp 1xxv 1ypt 1ytn 1yts 1ytw 2i42 3blt 3blu 3bm8 3f99 3f9a 3f9b 4gf3 4yaa 4z6b 4zi4 4zn5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3U96)