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(-) Description

Title :  STRUCTURE OF THE TANDEMLY REPEATED PROTEIN TYROSINE PHOSPHATASE LIKE PHYTASE FROM MITSUOKELLA MULTACIDA
 
Authors :  R. J. Gruninger, L. B. Selinger, S. C. Mosimann
Date :  31 Oct 08  (Deposition) - 09 Jun 09  (Release) - 29 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phytase, Tandem Repeat, Protein Tyrosine Phosphatase, Inositol Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. J. Gruninger, L. B. Selinger, S. C. Mosimann
Structural Analysis Of A Multifunctional, Tandemly Repeated Inositol Polyphosphatase.
J. Mol. Biol. V. 392 75 2009
PubMed-ID: 19500593  |  Reference-DOI: 10.1016/J.JMB.2009.05.079
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHYTASE
    Chains: A, B
    EC Number: 3.1.3.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PHYA, PHYAMM
    Organism Scientific: MITSUOKELLA MULTACIDA
    Organism Taxid: 52226
    Strain: O32

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2PO44Ligand/IonPHOSPHATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:221 , CYS A:250 , TYR A:251 , ALA A:252 , GLY A:253 , MET A:254 , GLY A:255 , ARG A:256BINDING SITE FOR RESIDUE PO4 A 1
02AC2SOFTWAREASP A:519 , CYS A:548 , GLN A:549 , ALA A:550 , GLY A:551 , ALA A:552 , GLY A:553 , ARG A:554BINDING SITE FOR RESIDUE PO4 A 2
03AC3SOFTWAREPHE A:275 , GLN A:313 , ASP A:317 , LYS B:337BINDING SITE FOR RESIDUE EDO A 5
04AC4SOFTWAREVAL A:331 , LYS A:334 , LYS A:335BINDING SITE FOR RESIDUE EDO A 6
05AC5SOFTWAREGLU A:164 , THR A:202 , GLU A:203 , GLU A:204 , TYR A:214 , ARG A:216BINDING SITE FOR RESIDUE EDO A 7
06AC6SOFTWARETYR A:237 , LYS A:268BINDING SITE FOR RESIDUE EDO A 8
07AC7SOFTWAREASP B:221 , CYS B:250 , TYR B:251 , ALA B:252 , MET B:254 , GLY B:255 , ARG B:256BINDING SITE FOR RESIDUE PO4 B 3
08AC8SOFTWAREASP B:519 , CYS B:548 , GLN B:549 , ALA B:550 , GLY B:551 , ALA B:552 , GLY B:553 , ARG B:554BINDING SITE FOR RESIDUE PO4 B 4
09AC9SOFTWARELYS A:337 , EDO B:10 , GLN B:313 , ASP B:317 , HOH B:650BINDING SITE FOR RESIDUE EDO B 9
10BC1SOFTWAREEDO B:9 , ASP B:276BINDING SITE FOR RESIDUE EDO B 10
11BC2SOFTWAREMET B:88 , PRO B:89 , THR B:90 , ASP B:277 , HOH B:774BINDING SITE FOR RESIDUE EDO B 641

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F41)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F41)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F41)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F41)

(-) Exons   (0, 0)

(no "Exon" information available for 3F41)

(-) 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:590
 aligned with A3QMF6_9FIRM | A3QMF6 from UniProtKB/TrEMBL  Length:640

    Alignment length:590
                                    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       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636
         A3QMF6_9FIRM    47 PAVVKNPPKLALKIDRADVNQLPRNFRMGSDKYVGVTKTGIMPTRKGMDTMNVSASSCFSEKELEAILKKVPVKPSQFYDVDLRGESHGYLNGTAVSWFANHDWGNDGRTEDIIIPLEKEQLASLKGSTVKSIYRFDDKKNVILSPVYVNYNKVRTEEEMVKQHGANYFRLTLQDHFRPDDPDVDKFLEFYKSLPKDAWLHYHCYAGMGRTTIFMVMHDILKNAKDVSFDDIIQRQKLIGIVDLSEIPDKKKNYGRKAYIERYQFVQHFYDYVKENPDLKTPYSVWAKKNKVNSWEPDYNGYIWRLDTKDRNQLPRNFRTMNSAFRTDVNVKKTGKGFTPTPTRKGLDTLYMSGSAEFSNGELQAMLPVLKQQAKGPIYIMDLRQETHGVFNGNAVSWYGLRDWGNLGKNKAEVLKDENSRLNAARGKSLIVAELDKDKMPIDPKPVKIESVMTEQQLVEKNGLHYYRIAATDHIWPSAANIDEFINFTRTMPANAWLHFHCQAGAGRTTAYMAMYDMMKNPDVSLGDILSRQYLLGGNYVAYEIAKPKPDQWKADYYHQKAHMIEKFYQYVQENHADGFKTSWSQWLAA 636
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee..........ee........................eeee...hhhhhhhhhhhh..hhh.eeeeeee...eeee..eeeeeehhhhh.....hhhhhhhhhhhhhhh.....eeeeeeee....eeeeeeeee...eehhhhhhhh...eeeeeee......hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..........eeeeeeee..........ee.........hhhhh.................eeee...hhhhhhhhhhhhhhhh...eeeeeee...eeee..eeeeeee.hhh.....hhhhhhhhhhhhhhhhh..eeeee............eee...eehhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh........hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f41 A  47 PAVVKNPPKLALKIDRADVNQLPRNFRMGSDKYVGVTKTGIMPTRKGMDTMNVSASSCFSEKELEAILKKVPVKPSQFYDVDLRGESHGYLNGTAVSWFANHDWGNDGRTEDIIIPLEKEQLASLKGSTVKSIYRFDDKKNVILSPVYVNYNKVRTEEEMVKQHGANYFRLTLQDHFRPDDPDVDKFLEFYKSLPKDAWLHYHCYAGMGRTTIFMVMHDILKNAKDVSFDDIIQRQKLIGIVDLSEIPDKKKNYGRKAYIERYQFVQHFYDYVKENPDLKTPYSVWAKKNKVNSWEPDYNGYIWRLDTKDRNQLPRNFRTMNSAFRTDVNVKKTGKGFTPTPTRKGLDTLYMSGSAEFSNGELQAMLPVLKQQAKGPIYIMDLRQETHGVFNGNAVSWYGLRDWGNLGKNKAEVLKDENSRLNAARGKSLIVAELDKDKMPIDPKPVKIESVMTEQQLVEKNGLHYYRIAATDHIWPSAANIDEFINFTRTMPANAWLHFHCQAGAGRTTAYMAMYDMMKNPDVSLGDILSRQYLLGGNYVAYEIAKPKPDQWKADYYHQKAHMIEKFYQYVQENHADGFKTSWSQWLAA 636
                                    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       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636


Chain B from PDB  Type:PROTEIN  Length:590
 aligned with A3QMF6_9FIRM | A3QMF6 from UniProtKB/TrEMBL  Length:640

    Alignment length:590
                                    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       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636
         A3QMF6_9FIRM    47 PAVVKNPPKLALKIDRADVNQLPRNFRMGSDKYVGVTKTGIMPTRKGMDTMNVSASSCFSEKELEAILKKVPVKPSQFYDVDLRGESHGYLNGTAVSWFANHDWGNDGRTEDIIIPLEKEQLASLKGSTVKSIYRFDDKKNVILSPVYVNYNKVRTEEEMVKQHGANYFRLTLQDHFRPDDPDVDKFLEFYKSLPKDAWLHYHCYAGMGRTTIFMVMHDILKNAKDVSFDDIIQRQKLIGIVDLSEIPDKKKNYGRKAYIERYQFVQHFYDYVKENPDLKTPYSVWAKKNKVNSWEPDYNGYIWRLDTKDRNQLPRNFRTMNSAFRTDVNVKKTGKGFTPTPTRKGLDTLYMSGSAEFSNGELQAMLPVLKQQAKGPIYIMDLRQETHGVFNGNAVSWYGLRDWGNLGKNKAEVLKDENSRLNAARGKSLIVAELDKDKMPIDPKPVKIESVMTEQQLVEKNGLHYYRIAATDHIWPSAANIDEFINFTRTMPANAWLHFHCQAGAGRTTAYMAMYDMMKNPDVSLGDILSRQYLLGGNYVAYEIAKPKPDQWKADYYHQKAHMIEKFYQYVQENHADGFKTSWSQWLAA 636
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee..........ee........................eeee...hhhhhhhhhhhh..hhh.eeeeeee...eeee..eeeeeehhhhh.....hhhhhhhhhhhhhhh.....eeeeeeee....eeeeeeeee...eehhhhhhhh...eeeeeee......hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..........eeeeeeee..........ee.........hhhhh.................eeee...hhhhhhhhhhhhhhhh...eeeeeee...eeee..eeeeeee.hhh.....hhhhhhhhhhhhhhhh...eeeee............eee...eehhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh...hhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f41 B  47 PAVVKNPPKLALKIDRADVNQLPRNFRMGSDKYVGVTKTGIMPTRKGMDTMNVSASSCFSEKELEAILKKVPVKPSQFYDVDLRGESHGYLNGTAVSWFANHDWGNDGRTEDIIIPLEKEQLASLKGSTVKSIYRFDDKKNVILSPVYVNYNKVRTEEEMVKQHGANYFRLTLQDHFRPDDPDVDKFLEFYKSLPKDAWLHYHCYAGMGRTTIFMVMHDILKNAKDVSFDDIIQRQKLIGIVDLSEIPDKKKNYGRKAYIERYQFVQHFYDYVKENPDLKTPYSVWAKKNKVNSWEPDYNGYIWRLDTKDRNQLPRNFRTMNSAFRTDVNVKKTGKGFTPTPTRKGLDTLYMSGSAEFSNGELQAMLPVLKQQAKGPIYIMDLRQETHGVFNGNAVSWYGLRDWGNLGKNKAEVLKDENSRLNAARGKSLIVAELDKDKMPIDPKPVKIESVMTEQQLVEKNGLHYYRIAATDHIWPSAANIDEFINFTRTMPANAWLHFHCQAGAGRTTAYMAMYDMMKNPDVSLGDILSRQYLLGGNYVAYEIAKPKPDQWKADYYHQKAHMIEKFYQYVQENHADGFKTSWSQWLAA 636
                                    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       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636
   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  (0, 0)

(no "SCOP Domain" information available for 3F41)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F41)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F41)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A3QMF6_9FIRM | A3QMF6)
molecular function
    GO:0016158    3-phytase activity    Catalysis of the reaction: myo-inositol hexakisphosphate + H2O = D-myo-inositol 1,2,4,5,6-pentakisphosphate + phosphate.
    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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  3f41
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  3.1.3.8
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 Related Entries

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

UniProtKB/TrEMBL
        A3QMF6_9FIRM | A3QMF6: 4wu3

(-) Related Entries Specified in the PDB File

2psz PTP LIKE PHYTASE FROM SELENOMONAS RUMINANTIUM