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(-) Description

Title :  STRUCTURE OF THE PTP-LIKE PHYTASE EXPRESSED BY SELENOMONAS RUMINANTIUM AT AN IONIC STRENGTH OF 500 MM
 
Authors :  R. J. Gruninger, L. B. Selinger, S. C. Mosimann
Date :  05 May 08  (Deposition) - 24 Jun 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ptp, Protein Tyrosine Phosphatase, Phytase, P-Loop, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. J. Gruninger, L. Brent Selinger, S. C. Mosimann
Effect Of Ionic Strength And Oxidation On The P-Loop Conformation Of The Protein Tyrosine Phosphatase-Like Phytase, Phyasr.
Febs J. V. 275 3783 2008
PubMed-ID: 18573100  |  Reference-DOI: 10.1111/J.1742-4658.2008.06524.X

(-) Compounds

Molecule 1 - MYO-INOSITOL HEXAPHOSPHATE PHOSPHOHYDROLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: PHYA
    Organism Scientific: SELENOMONAS RUMINANTIUM

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:42 , ARG B:310 , ALA B:346 , HOH B:523BINDING SITE FOR RESIDUE GOL B 400
2AC2SOFTWARETYR A:239 , PRO A:243 , GLN A:244 , LYS A:270 , HOH A:604 , HOH A:742BINDING SITE FOR RESIDUE GOL A 401
3AC3SOFTWARETYR B:239 , PRO B:243 , GLN B:244 , ALA B:246 , LYS B:270 , HOH B:488 , HOH B:501 , HOH B:549BINDING SITE FOR RESIDUE GOL B 402
4AC4SOFTWARETYR B:42 , LYS B:123 , THR B:124 , ALA B:125 , LYS B:307 , ARG B:310BINDING SITE FOR RESIDUE GOL B 403
5AC5SOFTWARELYS B:83 , PHE B:289 , PHE B:294 , LYS B:297BINDING SITE FOR RESIDUE GOL B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D1H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3D1H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D1H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D1H)

(-) Exons   (0, 0)

(no "Exon" information available for 3D1H)

(-) 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:313
 aligned with Q7WUJ1_SELRU | Q7WUJ1 from UniProtKB/TrEMBL  Length:346

    Alignment length:313
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343   
         Q7WUJ1_SELRU    34 TVTEPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGMDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGMRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHCEAGVGRTTAFMVMTDMLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVMIEQFYRYVQENRADGYQTPWSVWLKSHPAKA 346
               SCOP domains d3d1ha_ A: Myo-inositol hexaphosphate phosphohydrolase (phytase) PhyA                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh...eeee............ee........hhhhh..........hhhhhheeee...hhhhhhhhhhhhhh.....eeeeeee...eeee..eeeeeehhhhh.....hhhhhhhhhhhhhhhhh..eeeee..hhhhh....eeee...eehhhhhhhhh..eeeeeee......hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhh...hhhhhhhhhhhh............hhhhh.hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d1h A  34 TVTEPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGMDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGMRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHCEAGVGRTTAFMVMTDMLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVMIEQFYRYVQENRADGYQTPWSVWLKSHPAKA 346
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343   


Chain B from PDB  Type:PROTEIN  Length:313
 aligned with Q7WUJ1_SELRU | Q7WUJ1 from UniProtKB/TrEMBL  Length:346

    Alignment length:313
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343   
         Q7WUJ1_SELRU    34 TVTEPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGMDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGMRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHCEAGVGRTTAFMVMTDMLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVMIEQFYRYVQENRADGYQTPWSVWLKSHPAKA 346
               SCOP domains d3d1hb_ B: Myo-inositol hexaphosphate phosphohydrolase (phytase) PhyA                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.eeeeee............ee........hhhhh..........hhhhhheeee...hhhhhhhhhhhhhh.....eeeeeee...eeee..eeeeeee.hhh.....hhhhhhhhhhhhhhhhh..eeeee..hhhhh....eeee...eehhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh...hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d1h B  34 TVTEPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGMDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGMRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHCEAGVGRTTAFMVMTDMLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVMIEQFYRYVQENRADGYQTPWSVWLKSHPAKA 346
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "CATH Domain" information available for 3D1H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D1H)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7WUJ1_SELRU | Q7WUJ1)
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:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.

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 Related Entries

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

UniProtKB/TrEMBL
        Q7WUJ1_SELRU | Q7WUJ1: 1u24 1u25 1u26 2b4o 2b4p 2b4u 2psz 2pt0 3d1o 3d1q 3mmj 3moz 3o3l 4wty 4wu2

(-) Related Entries Specified in the PDB File

1u24 CRYSTAL STRUCTURE OF SELENOMONAS RUMINANTIUM PHYTASE WITH OPEN P-LOOP
2b4p STRUCTURE OF THE D223N MUTANT OF SELENOMONAS RUMINANTIUM
2b4u STRUCTURE OF THE C252S MUTANT OF SELENOMONAS RUMINANTIUM
2psz STRUCTURE OF THE PTP-LIKE PHYTASE EXPRESSED BY SELENOMONAS RUMINANTIUM AT LOW IONIC STRENGTH
2pt0 STRUCTURE OF SELENOMONAS RUMINANTIUM PTP-LIKE PHYTASE WITH THE ACTIVE SITE CYSTEINE OXIDIZED TO CYSTEINE-SULFONIC ACID
3d1o
3d1q