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(-) Description

Title :  STRUCTURE OF THE C252S 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) - 20 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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_C252S
    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  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MLI2Ligand/IonMALONATE ION
3MSE12Mod. Amino AcidSELENOMETHIONINE
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MLI1Ligand/IonMALONATE ION
3MSE6Mod. Amino AcidSELENOMETHIONINE
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MLI1Ligand/IonMALONATE ION
3MSE6Mod. Amino AcidSELENOMETHIONINE
4SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:223 , SER A:252 , GLU A:253 , ALA A:254 , GLY A:255 , VAL A:256 , GLY A:257 , ARG A:258 , HOH A:466 , HOH A:681 , MLI A:1042BINDING SITE FOR RESIDUE SO4 A 348
2AC2SOFTWAREASP B:223 , SER B:252 , GLU B:253 , ALA B:254 , GLY B:255 , VAL B:256 , GLY B:257 , ARG B:258 , HOH B:465 , HOH B:513 , MLI B:1041BINDING SITE FOR RESIDUE SO4 B 349
3AC3SOFTWAREGLN A:161 , HOH A:447BINDING SITE FOR RESIDUE CL A 350
4AC4SOFTWAREHIS B:224 , VAL B:256 , GLY B:257 , LYS B:305 , TYR B:309 , LYS B:312 , SO4 B:349 , HOH B:742BINDING SITE FOR RESIDUE MLI B 1041
5AC5SOFTWAREHIS A:224 , GLY A:257 , PHE A:289 , TYR A:309 , LYS A:312 , SO4 A:348 , HOH A:466BINDING SITE FOR RESIDUE MLI A 1042

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B4U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B4U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B4U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B4U)

(-) Exons   (0, 0)

(no "Exon" information available for 2B4U)

(-) 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:314
 aligned with Q7WUJ1_SELRU | Q7WUJ1 from UniProtKB/TrEMBL  Length:346

    Alignment length:314
                                                                                                                                                                                                                                                                                                                                                  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  | 
         Q7WUJ1_SELRU    34 TVTEPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGMDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGMRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHCEAGVGRTTAFMVMTDMLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVMIEQFYRYVQENRADGYQTPWSVWLKSHPAKA-   -
               SCOP domains d2b4ua_ A: automated matches                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.eeeeee............ee........hhhhh................eeee...hhhhhhhhhhhhhh.....eeeeeee...eeee..eeeeeee.hhh.....hhhhhhhhhhhhhhhhh..eeeee...........eeee...eehhhhhhhhh..eeeeeee......hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhh...hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b4u A  34 TVTEPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGmDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGmRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHSEAGVGRTTAFmVmTDmLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVmIEQFYRYVQENRADGYQTPWSVWLKSHPAKAL 347
                                    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    
                                                                                          97-MSE                                                                                                              214-MSE                                          263-MSE|                                            315-MSE                            
                                                                                                                                                                                                                                                                 265-MSE                                                                              
                                                                                                                                                                                                                                                                    268-MSE                                                                           


Chain B from PDB  Type:PROTEIN  Length:314
 aligned with Q7WUJ1_SELRU | Q7WUJ1 from UniProtKB/TrEMBL  Length:346

    Alignment length:314
                                                                                                                                                                                                                                                                                                                                                  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  | 
         Q7WUJ1_SELRU    34 TVTEPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGMDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGMRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHCEAGVGRTTAFMVMTDMLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVMIEQFYRYVQENRADGYQTPWSVWLKSHPAKA-   -
               SCOP domains d2b4ub_ B: automated matches                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.eeeeee............ee........hhhhh................eeee...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
                 2b4u B  34 TVTEPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGmDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGmRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHSEAGVGRTTAFmVmTDmLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVmIEQFYRYVQENRADGYQTPWSVWLKSHPAKAL 347
                                    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    
                                                                                          97-MSE                                                                                                              214-MSE                                          263-MSE|                                            315-MSE                            
                                                                                                                                                                                                                                                                 265-MSE                                                                              
                                                                                                                                                                                                                                                                    268-MSE
   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 2B4U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B4U)

(-) 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 2b4o 2b4p 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
2b4o STRUCTURE OF THE R258K ACTIVE SITE MUTANT OF SELENOMONAS RUMINANTIUM PTP-LIKE PHYTASE
2b4p STRUCTURE OF THE D223N ACTIVE SITE MUTANT OF SELENOMONAS RUMINANTIUM PTP-LIKE PHYTASE