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(-) Description

Title :  CRYSTAL STRUCTURE OF PHYTASE WITH MAGNESIUM FROM BACILLUS AMYLOLIQUEFACIENS
 
Authors :  S. Shin, N. -C. Ha, B. -H. Oh
Date :  31 Aug 99  (Deposition) - 03 Feb 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphomonoesterase, Phytase, Thermostable, Phosphatase, Calcium, Magnesium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. -C. Ha, B. -C. Oh, S. Shin, H. J. Kim, T. K. Oh, Y. O. Kim, K. Y. Choi, B. H. Oh
Crystal Structures Of A Novel, Thermostable Phytase In Partially And Fully Calcium-Loaded States
Nat. Struct. Biol. V. 7 147 2000
PubMed-ID: 10655618  |  Reference-DOI: 10.1038/72421

(-) Compounds

Molecule 1 - 3-PHYTASE
    Cellular Location: SECRETION
    Chains: A
    EC Number: 3.1.3.8
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Taxid: 1423
    Organism Scientific: BACILLUS AMYLOLIQUEFACIENS
    Organism Taxid: 1390
    Other Details: CALCIUM MAGNESIUM
    Strain: DS11
    Synonym: PHYTASE, PHYTATE 3-PHOSPHATASE, MYO-INOSITOL-HEXAPHOSPHATE 3-PHOSPHOHYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:43 , ASP A:308 , ASN A:339 , ILE A:340 , ASP A:341BINDING SITE FOR RESIDUE CA A 801
2AC2SOFTWAREASP A:308 , GLY A:309 , ASN A:336 , GLU A:338 , HOH A:2015 , HOH A:2031BINDING SITE FOR RESIDUE CA A 802
3AC3SOFTWAREASP A:56 , PRO A:57 , VAL A:101 , HOH A:2007 , HOH A:2017 , HOH A:2033BINDING SITE FOR RESIDUE CA A 803
4AC4SOFTWARETYR A:159 , GLU A:211 , GLU A:227 , GLU A:260BINDING SITE FOR RESIDUE MG A 901
5AC5SOFTWAREASP A:258 , GLU A:260 , GLN A:279BINDING SITE FOR RESIDUE MG A 902

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:32 -Pro A:33
2Pro A:257 -Asp A:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QLG)

(-) 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:353
 aligned with PHYT_BACSD | O66037 from UniProtKB/Swiss-Prot  Length:383

    Alignment length:353
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378   
           PHYT_BACSD    29 KLSDPYHFTVNAAAETEPVDTAGDAADDPAIWLDPKNPQNSKLITTNKKSGLAVYSLEGKMLHSYHTGKLNNVDIRYDFPLNGKKVDIAAASNRSEGKNTIEIYAIDGKNGTLQSITDPNRPIASAIDEVYGFSLYHSQKTGKYYAMVTGKEGEFEQYELNADKNGYISGKKVRAFKMNSQTEGMAADDEYGSLYIAEEDEAIWKFSAEPDGGSNGTVIDRADGRHLTPDIEGLTIYYAADGKGYLLASSQGNSSYAIYERQGQNKYVADFQITDGPETDGTSDTDGIDVLGFGLGPEYPFGLFVAQDGENIDHGQKANQNFKMVPWERIADKIGFHPQVNKQVDPRKMTDRS 381
               SCOP domains d1qlga_ A: Thermostable phytase (3-phytase)                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1qlgA00 A:29-381  [code=2.120.10.20, no name defined]                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains Phytase-1qlgA01 A:29-381                                                                                                                                                                                                                                                                                                                                          Pfam domains
         Sec.struct. author ......eeee..................eeee....hhhhheeee.......eee.....eeee........eeee..eee..eee.eeeeee.hhhh.eeeeeeee....eeee.................eeeee......eeeeee....eeeeeeeee.....eeeeeeeeee.......eeee....eeeeee...eeeeee.hhhhh...eeeee............eeeee.....eeeeeee.hhheeeeee......eeeeeee..............eeee...........eeeeee..eee..eee..eeeeeehhhhhhh...........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qlg A  29 KLSDPYHFTVNAAAETEPVDTAGDAADDPAIWLDPKNPQNSKLITTNKKSGLAVYSLEGKMLHSYHTGKLNNVDIRYDFPLNGKKVDIAAASNRSEGKNTIEIYAIDGKNGTLQSITDPNRPIASAIDEVYGFSLYHSQKTGKYYAMVTGKEGEFEQYELNADKNGYISGKKVRAFKMNSQTEGMAADDEYGSLYIAEEDEAIWKFSAEPDGGSNGTVIDRADGRHLTPDIEGLTIYYAADGKGYLLASSQGNSSYAIYERQGQNKYVADFQITDGPETDGTSDTDGIDVLGFGLGPEYPFGLFVAQNGENIDHGQKANQNFKMVPWERIADKIGFHPQVNKQVDPRKMTDRS 381
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378
   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, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Phytase] (3)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PHYT_BACSD | O66037)
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.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  Cis Peptide Bonds
    Asp A:32 - Pro A:33   [ RasMol ]  
    Pro A:257 - Asp A:258   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PHYT_BACSD | O66037: 1cvm 1h6l 1poo 2poo

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QLG)