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(-) Description

Title :  CADMIUM INHIBITED CRYSTAL STRUCTURE OF PHYTASE FROM BACILLUS AMYLOLIQUEFACIENS
 
Authors :  S. Shin, N. -C. Ha, B. -H. Oh
Date :  24 Aug 99  (Deposition) - 24 Feb 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Thermostable Bacillus Phytase Phytate Phosphatase Cadmium Calcium, Hydrolase (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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHYTASE
    Chains: A
    EC Number: 3.1.3.8
    Organism Scientific: BACILLUS AMYLOLIQUEFACIENS
    Organism Taxid: 1390
    Strain: DS11

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2CD5Ligand/IonCADMIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:43 , ASP A:308 , ASN A:339 , ILE A:340 , ASP A:341 , HOH A:529BINDING SITE FOR RESIDUE CA A 801
2AC2SOFTWAREASP A:308 , GLY A:309 , ASN A:336 , GLU A:338 , HOH A:507 , HOH A:554BINDING SITE FOR RESIDUE CA A 802
3AC3SOFTWAREASP A:56 , PRO A:57 , VAL A:101 , HOH A:515 , HOH A:526 , HOH A:533BINDING SITE FOR RESIDUE CA A 803
4AC4SOFTWARETYR A:159 , GLU A:211 , GLU A:227 , GLU A:260BINDING SITE FOR RESIDUE CD A 811
5AC5SOFTWAREASP A:258 , GLU A:260 , GLN A:279BINDING SITE FOR RESIDUE CD A 812
6AC6SOFTWAREASP A:55 , GLU A:211BINDING SITE FOR RESIDUE CD A 813
7AC7SOFTWAREASP A:52 , LYS A:76 , ASP A:314BINDING SITE FOR RESIDUE CD A 814
8AC8SOFTWARELYS A:29 , ASP A:228 , ASP A:258BINDING SITE FOR RESIDUE CD A 815

(-) SS Bonds  (0, 0)

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

(-) 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 1CVM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1CVM)

(-) 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 d1cvma_ A: Thermostable phytase (3-phytase)                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1cvmA00 A:29-381  [code=2.120.10.20, no name defined]                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...ee..........eeeeeee....hhhh.eeeeee.....eeee....eeee.....eeeeeeeeeeee..eeeeeeeeee.hhhh.eeeeeee......eee..............eeeeeeee......eeeeeee...eeeeeeeee.....eeeeeeeeee....eeeeeee....eeeeee...eeeeee.hhhhh...eeeee.........eeeeeeee.....eeeeeee....eeeeee......eeeeeee..............eeee...........eeeeee...ee..ee...eeeeeehhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cvm 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  (0, 0)

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

(-) 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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    Asp A:32 - Pro A:33   [ RasMol ]  
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1poo NATIVE STRUCTURE