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(-) Description

Title :  CRYSTAL STRUCTURES OF BACILLUS SUBTILIS ALKALINE PHYTASE IN COMPLEX WITH CA2+, CD2+, CO2+, NI2+, MG2+ AND MYO-INOSITOL HEXASULFATE
 
Authors :  Y. F. Zeng, T. P. Ko, H. L. Lai, Y. S. Cheng, T. H. Wu, Y. Ma, C. S. Yang, K. J. C C. H. Huang, R. T. Guo, J. R. Liu
Date :  22 Aug 10  (Deposition) - 13 Apr 11  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Propeller, Phytase, Phytate, Myo-Inositol Hexasulfate, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. F. Zeng, T. P. Ko, H. L. Lai, Y. S. Cheng, T. H. Wu, Y. Ma, C. C. Chen, C. S. Yang, K. J. Cheng, C. H. Huang, R. T. Guo, J. R. Liu
Crystal Structures Of Bacillus Alkaline Phytase In Complex With Divalent Metal Ions And Inositol Hexasulfate
J. Mol. Biol. V. 409 214 2011
PubMed-ID: 21463636  |  Reference-DOI: 10.1016/J.JMB.2011.03.063

(-) Compounds

Molecule 1 - 3-PHYTASE
    Chains: A
    EC Number: 3.1.3.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32 XA/LIC
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PHYC, PHYB13
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: ALKALINE PHYTASE, BETA-PROPELLER PHYTASE, BACILLUS 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  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CD7Ligand/IonCADMIUM ION
3IHS1Ligand/IonD-MYO-INOSITOL-HEXASULPHATE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:24 , LYS A:48 , LYS A:49 , ARG A:94 , TYR A:131 , LYS A:151 , GLU A:183 , ASP A:230 , GLU A:232 , GLN A:251 , ASP A:286 , HOH A:405 , HOH A:451 , HOH A:532 , HOH A:752 , CD A:904 , CD A:905 , CD A:906 , CD A:907BINDING SITE FOR RESIDUE IHS A 4000
02AC2SOFTWAREGLU A:15 , ASP A:280 , ASN A:311 , ILE A:312 , ASP A:313 , HOH A:401BINDING SITE FOR RESIDUE CA A 901
03AC3SOFTWAREASP A:280 , GLY A:281 , ASP A:308 , GLU A:310 , HOH A:402 , HOH A:445BINDING SITE FOR RESIDUE CA A 902
04AC4SOFTWAREASP A:28 , PRO A:29 , VAL A:73 , HOH A:409 , HOH A:410 , HOH A:488BINDING SITE FOR RESIDUE CA A 903
05AC5SOFTWAREASP A:27 , GLU A:183 , ASP A:286 , HOH A:451 , HOH A:547 , IHS A:4000BINDING SITE FOR RESIDUE CD A 904
06AC6SOFTWARETYR A:131 , GLU A:183 , GLU A:199 , GLU A:232 , HOH A:527 , IHS A:4000BINDING SITE FOR RESIDUE CD A 905
07AC7SOFTWAREASP A:230 , GLU A:232 , GLN A:251 , HOH A:527 , IHS A:4000BINDING SITE FOR RESIDUE CD A 906
08AC8SOFTWAREASP A:24 , ASP A:286 , HOH A:405 , HOH A:529 , HOH A:530 , IHS A:4000BINDING SITE FOR RESIDUE CD A 907
09AC9SOFTWAREASP A:200 , ASP A:230 , HOH A:448 , HOH A:449 , HOH A:450 , HOH A:528BINDING SITE FOR RESIDUE CD A 908
10BC1SOFTWAREASP A:220 , HIS A:226 , HOH A:500 , HOH A:501 , HOH A:502BINDING SITE FOR RESIDUE CD A 909
11BC2SOFTWAREHIS A:121 , GLU A:201 , HOH A:522 , HOH A:523 , HOH A:524 , HOH A:702BINDING SITE FOR RESIDUE CA A 910
12BC3SOFTWAREHIS A:314 , HOH A:442 , HOH A:443BINDING SITE FOR RESIDUE CD A 911

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:4 -Pro A:5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3AMS)

(-) 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:352
 aligned with PHYC_BACIU | O31097 from UniProtKB/Swiss-Prot  Length:383

    Alignment length:352
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379  
           PHYC_BACIU    30 LSDPYHFTVNAAAETEPVDTAGDAADDPAIWLDPKTPQNSKLITTNKKSGLVVYSLDGKMLHSYNTGKLNNVDIRYDFPLNGKKVDIAAASNRSEGKNTIEIYAIDGKNGTLQSMTDPDHPIATAINEVYGFTLYHSQKTGKYYAMVTGKEGEFEQYELKADKNGYISGKKVRAFKMNSQTEGMAADDEYGRLYIAEEDEAIWKFSAEPDGGSNGTVIDRADGRHLTRDIEGLTIYYAADGKGYLMASSQGNSSYAIYDRQGKNKYVADFRITDGPETDGTSDTDGIDVLGFGLGPEYPFGIFVAQDGENIDHGQKANQNFKIVPWERIADQIGFRPLANEQVDPRKLTDRS 381
               SCOP domains d3amsa_ A: automated matches                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..ee...............ee....hhhh.eeeeee...eeeeee....eeeee....eeeeeeeeeeee..eeeeeeeeee......eeeeeee......eee.......ee........eeeee......eeeeee....eeeeeeeee.....eeeeeeeeee....eeeeeee....eeeeee...eeeeee.........eeeee.........eeeeeeee.hhh.eeeeeee.hhheeeeee......eeeeeeee.............eeee...........eeeeee...ee..ee...eeeeeehhhhhhhh....hhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ams A   2 LSDPYHFTVNAAAETEPVDTAGDAADDPAIWLDPKTPQNSKLITTNKKSGLVVYSLDGKMLHSYNTGKLNNVDIRYDFPLNGKKVDIAAASNRSEGKNTIEIYAIDGKNGTLQSMTDPDHPIATAINEVYGFTLYHSQKTGKYYAMVTGKEGEFEQYELKADKNGYISGKKVRAFKMNSQTEGMAADDEYGRLYIAEEDEAIWKFSAEPDGGSNGTVIDRADGRHLTRDIEGLTIYYAADGKGYLMASSQGNSSYAIYDRQGKNKYVADFRITDGPETDGTSDTDGIDVLGFGLGPEYPFGIFVAQDGENIDHGQKANQNFKIVPWERIADQIGFRPLANEQVDPRKLTDRS 353
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351
   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PHYC_BACIU | O31097)
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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        PHYC_BACIU | O31097: 3amr

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3amr