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(-) Description

Title :  STRUCTURE OF THE R258K MUTANT OF SELENOMONAS RUMINANTIUM PTP-LIKE PHYTASE
 
Authors :  R. J. Gruninger, L. B. Selinger, S. C. Mosimann
Date :  26 Sep 05  (Deposition) - 07 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ptp-Like, Ionic Strength, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Puhl, R. J. Gruninger, R. Greiner, T. W. Janzen, S. C. Mosimann, L. B. Selinger
Kinetic And Structural Analysis Of A Bacterial Protein Tyrosine Phosphatase-Like Myo-Inositol Polyphosphatase.
Protein Sci. V. 16 1368 2007
PubMed-ID: 17567745  |  Reference-DOI: 10.1110/PS.062738307

(-) Compounds

Molecule 1 - MYO-INOSITOL HEXAPHOSPHATE PHOSPHOHYDROLASE
    Chains: A, B
    EC Number: 3.1.3.72
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PHYASR_R252K
    Mutation: YES
    Organism Scientific: SELENOMONAS RUMINANTIUM
    Organism Taxid: 971

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:160BINDING SITE FOR RESIDUE CL A 401
2AC2SOFTWAREGLN B:161BINDING SITE FOR RESIDUE CL B 402
3AC3SOFTWARELEU B:77 , ARG B:94BINDING SITE FOR RESIDUE CL B 403
4AC4SOFTWAREASP A:223 , HIS A:224 , GLY A:257 , LYS A:258 , HOH A:457BINDING SITE FOR RESIDUE CL A 404
5AC5SOFTWAREHIS B:101 , GLN B:244 , ASP B:245 , HOH B:543BINDING SITE FOR RESIDUE CL B 405
6AC6SOFTWARETHR B:333BINDING SITE FOR RESIDUE CL B 406
7AC7SOFTWARETYR A:239 , PRO A:243 , GLN A:244 , ALA A:246 , LYS A:270 , HOH A:731BINDING SITE FOR RESIDUE GOL A 399
8AC8SOFTWAREPRO B:243 , GLN B:244 , ALA B:246 , LYS B:270 , HOH B:439BINDING SITE FOR RESIDUE GOL B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B4O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B4O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B4O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B4O)

(-) Exons   (0, 0)

(no "Exon" information available for 2B4O)

(-) 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: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 d2b4oa_ A: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.eeeeee............ee........hhhhh..........hhhhhheeee...hhhhhhhhhhhhhh.....eeeee.....eeee..eeeeeee.hhh.....hhhhhhhhhhhhhhhh...eeeee..hhhhh....eeee...eehhhhhhhhh..eeee.........hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh...hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b4o A  34 TVTEPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGMDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGMRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHCEAGVGKTTAFMVMTDMLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVMIEQFYRYVQENRADGYQTPWSVWLKSHPAKA 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 d2b4ob_ B: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh...eeee............ee........hhhhh..........hhhhhheeee...hhhhhhhhhhhhhh.....eeeee.....eeee..eeeeeehhhhh.....hhhhhhhhhhhhhhhhh..eeeee..hhhhh....eeee...eehhhhhhhhh..eeee.........hhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhhh...hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b4o B  34 TVTEPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGMDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGMRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHCEAGVGKTTAFMVMTDMLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVMIEQFYRYVQENRADGYQTPWSVWLKSHPAKA 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)
  - → 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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2B4O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B4O)

(-) Gene Ontology  (5, 5)

Asymmetric 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 2b4p 2b4u 2psz 2pt0 3d1h 3d1o 3d1q 3mmj 3moz 3o3l 4wty 4wu2

(-) Related Entries Specified in the PDB File

1u24 CRYSTAL STRUCTURE OF SELENOMONAS RUMINANTIUM PHYTASE
1u25 CRYSTAL STRUCTURE OF SELENOMONAS RUMINANTIUM PHYTASE COMPLEXED WITH PERSULFATED PHYTATE IN THE C2221 CRYSTAL FORM
1u26 CRYSTAL STRUCTURE OF SELENOMONAS RUMINANTIUM PHYTASE COMPLEXED WITH PERSULFATED PHYTATE CLASSIFICATION HYDROLASE
2b4p STRUCTURE OF THE D223N ACTIVE SITE MUTANT OF SELENOMONAS RUMINANTIUM PTP-LIKE PHYTASE
2b4u STRUCTURE OF THE C252S MUTANT OF SELENOMONAS RUMINANTIUM PTP-LIKE PHYTASE