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(-) Description

Title :  CRYSTAL STRUCTURE OF SELENOMONAS RUMINANTIUM PHYTASE COMPLEXED WITH PERSULFATED PHYTATE IN THE C2221 CRYSTAL FORM
 
Authors :  H. M. Chu, R. T. Guo, T. W. Lin, C. C. Chou, H. L. Shr, H. L. Lai, T. Y. Tang, K. J. Cheng, B. L. Selinger, A. H. -J. Wang
Date :  16 Jul 04  (Deposition) - 09 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Ptp, P-Loop, Phytase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. M. Chu, R. T. Guo, T. W. Lin, C. C. Chou, H. L. Shr, H. L. Lai, T. Y. Tang, K. J. Cheng, B. L. Selinger, A. H. -J. Wang
Structures Of Selenomonas Ruminantium Phytase In Complex With Persulfated Phytate; Dsp Phytase Fold And Mechanism For Sequential Substrate Hydrolysis
Structure V. 12 2015 2004
PubMed-ID: 15530366  |  Reference-DOI: 10.1016/J.STR.2004.08.010
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MYO-INOSITOL HEXAPHOSPHATE PHOSPHOHYDROLASE
    Chains: A, B, C
    EC Number: 3.1.3.72
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: SELENOMONAS RUMINANTIUM
    Organism Taxid: 971
    Synonym: PHYTASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric Unit (2, 21)
No.NameCountTypeFull Name
1IHS3Ligand/IonD-MYO-INOSITOL-HEXASULPHATE
2MSE18Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1IHS2Ligand/IonD-MYO-INOSITOL-HEXASULPHATE
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1IHS-1Ligand/IonD-MYO-INOSITOL-HEXASULPHATE
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 7)
No.NameCountTypeFull Name
1IHS1Ligand/IonD-MYO-INOSITOL-HEXASULPHATE
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:71 , HIS A:74 , LYS A:286 , HOH A:3317 , ARG C:57 , LYS C:72 , LYS C:178 , VAL C:245 , LYS C:288 , ASP C:291 , LYS C:294 , TYR C:298BINDING SITE FOR RESIDUE IHS A 2165
2AC2SOFTWAREGLN A:150 , HIS A:151 , LEU A:154 , ARG A:158 , GLN A:195 , TYR A:205 , ARG A:207 , ARG A:223 , HOH A:2640 , HOH A:2664 , HOH A:3164BINDING SITE FOR RESIDUE IHS A 2167
3AC3SOFTWARELYS A:72 , LYS A:176 , VAL A:245 , LYS A:288 , LYS A:294 , HOH A:3316 , LYS C:71 , HIS C:74 , PRO C:284 , LYS C:286 , HOH C:2552 , HOH C:2812 , HOH C:3065BINDING SITE FOR RESIDUE IHS C 2166

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U25)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U25)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U25)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U25)

(-) Exons   (0, 0)

(no "Exon" information available for 1U25)

(-) 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:311
 aligned with Q7WUJ1_SELRU | Q7WUJ1 from UniProtKB/TrEMBL  Length:346

    Alignment length:311
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345 
         Q7WUJ1_SELRU    36 TEPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGMDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGMRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHCEAGVGRTTAFMVMTDMLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVMIEQFYRYVQENRADGYQTPWSVWLKSHPAKA 346
               SCOP domains d1u25a_ A: Myo-inositol hexaphosphate phosphohydrolase (phytase) PhyA                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh..eeee............ee........hhhhh..........hhhhhheeee...hhhhhhhhhhhhh......eeeeeee...eeee..eeeeeehhhhh.....hhhhhhhhhhhhhhhh...eeeee...........eeee...eehhhhhhhhh..eeeeeee......hhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhhh...hhhhhhhhhhhh...........ee..hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u25 A  25 TEPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGmDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGmRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHCEAGVGRTTAFmVmTDmLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVmIEQFYRYVQENRADGYQTPWSVWLKSHPAKA 335
                                    34        44        54        64        74        84 |      94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254  |    264       274       284       294       304       314       324       334 
                                                                                        86-MSE                                                                                                              203-MSE                                          252-MSE|                                            304-MSE                           
                                                                                                                                                                                                                                                               254-MSE                                                                             
                                                                                                                                                                                                                                                                  257-MSE                                                                          


Chain B from PDB  Type:PROTEIN  Length:312
 aligned with Q7WUJ1_SELRU | Q7WUJ1 from UniProtKB/TrEMBL  Length:346

    Alignment length:312
                                                                                                                                                                                                                                                                                                                                                346 
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345| 
         Q7WUJ1_SELRU    36 TEPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGMDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGMRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHCEAGVGRTTAFMVMTDMLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVMIEQFYRYVQENRADGYQTPWSVWLKSHPAKA-   -
               SCOP domains d1u25b_ B: 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.....hhhhhhhhhhhhhhh....eeeee..hhhhh....eeee...eehhhhhhhh...eeeeeee......hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh...hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1u25 B  25 TEPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGmDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGmRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHCEAGVGRTTAFmVmTDmLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVmIEQFYRYVQENRADGYQTPWSVWLKSHPAKAL 336
                                    34        44        54        64        74        84 |      94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254  |    264       274       284       294       304       314       324       334  
                                                                                        86-MSE                                                                                                              203-MSE                                          252-MSE|                                            304-MSE                            
                                                                                                                                                                                                                                                               254-MSE                                                                              
                                                                                                                                                                                                                                                                  257-MSE                                                                           


Chain C from PDB  Type:PROTEIN  Length:310
 aligned with Q7WUJ1_SELRU | Q7WUJ1 from UniProtKB/TrEMBL  Length:346

    Alignment length:310
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346
         Q7WUJ1_SELRU    37 EPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGMDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGMRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHCEAGVGRTTAFMVMTDMLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVMIEQFYRYVQENRADGYQTPWSVWLKSHPAKA 346
               SCOP domains d1u25c_ C: Myo-inositol hexaphosphate phosphohydrolase (phytase) PhyA                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh.eeeeee............ee........hhhhh................eeee...hhhhhhhhhhhhhhhh...eeeeeee...eeee..eeeeeee.hhh.....hhhhhhhhhhhhhhh....eeeee...........eeee...eehhhhhhhhhh.eeeeeee......hhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhhh...hhhhhhhhhhhh..........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u25 C  26 EPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGmDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGmRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHCEAGVGRTTAFmVmTDmLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVmIEQFYRYVQENRADGYQTPWSVWLKSHPAKA 335
                                    35        45        55        65        75        85|       95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245      |255 |     265       275       285       295       305       315       325       335
                                                                                       86-MSE                                                                                                              203-MSE                                          252-MSE|                                            304-MSE                           
                                                                                                                                                                                                                                                              254-MSE                                                                             
                                                                                                                                                                                                                                                                 257-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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1U25)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1U25)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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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  1u25
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  3.1.3.72
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 Related Entries

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

UniProtKB/TrEMBL
        Q7WUJ1_SELRU | Q7WUJ1: 1u24 1u26 2b4o 2b4p 2b4u 2psz 2pt0 3d1h 3d1o 3d1q 3mmj 3moz 3o3l 4wty 4wu2

(-) Related Entries Specified in the PDB File

1u24 THE SAME PROTEIN
1u26 THE SAME PROTEIN COMPLEXED WITH PERSULFATED PHYTATE