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(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 6.6 WITH HG2+ CATION ACTING AS AN INTERMOLECULAR BRIDGE
 
Authors :  D. Lim, S. Golovan, C. W. Forsberg, Z. Jia
Date :  08 Dec 99  (Deposition) - 02 Aug 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Histidine Acid Phosphatase Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Lim, S. Golovan, C. W. Forsberg, Z. Jia
Crystal Structures Of Escherichia Coli Phytase And Its Complex With Phytate.
Nat. Struct. Biol. V. 7 108 2000
PubMed-ID: 10655611  |  Reference-DOI: 10.1038/72371
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHYTASE
    ChainsA
    EC Number3.1.3.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A
    Expression System Taxid562
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymPH 2.5 ACID PHOSPHATASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1HG1Ligand/IonMERCURY (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:113 , ASP A:154 , HIS A:158 , TYR A:289 , HOH A:625BINDING SITE FOR RESIDUE HG A 500

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:77 -A:108
2A:133 -A:408
3A:178 -A:188
4A:382 -A:391

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:293 -Pro A:294

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HIS_ACID_PHOSPHAT_1PS00616 Histidine acid phosphatases phosphohistidine signature.PPA_ECOLI30-44  1A:8-22
2HIS_ACID_PHOSPHAT_2PS00778 Histidine acid phosphatases active site signature.PPA_ECOLI319-335  1A:297-313

(-) Exons   (0, 0)

(no "Exon" information available for 1DKM)

(-) 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:410
 aligned with PPA_ECOLI | P07102 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:410
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432
            PPA_ECOLI    23 QSEPELKLESVVIVSRHGVRAPTKATQLMQDVTPDAWPTWPVKLGWLTPRGGELIAYLGHYQRQRLVADGLLAKKGCPQSGQVAIIADVDERTRKTGEAFAAGLAPDCAITVHTQADTSSPDPLFNPLKTGVCQLDNANVTDAILSRAGGSIADFTGHRQTAFRELERVLNFPQSNLCLKREKQDESCSLTQALPSELKVSADNVSLTGAVSLASMLTEIFLLQQAQGMPEPGWGRITDSHQWNTLLSLHNAQFYLLQRTPEVARSRATPLLDLIKTALTPHPPQKQAYGVTLPTSVLFIAGHDTNLANLGGALELNWTLPGQPDNTPPGGELVFERWRRLSDNSQWIQVSLVFQTLQQMRDKTPLSLNTPPGEVKLTLAGCEERNAQGMCSLAGFTQIVNEARIPACSL 432
               SCOP domains d1dkma_ A: Phytase (myo-inositol-hexakisphosphate-3-phosphohydrolase)                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1dkmA01 A:1-134,A:259-410 Phosphoglycerate mutase-like                                                                                1dkmA02 A:135-258 Phosphoglycerate mutase-like                                                                              1dkmA01 A:1-134,A:259-410 Phosphoglycerate mutase-like                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee.........hhhhhhh...............hhhhhhhhhhhhhhhhhhhhhh.............eeeee..hhhhhhhhhhhhhhhh......ee........hhhhh.........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh...eee....eeehhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....eeee..eee...eeeeeehhhhhhhhhhhhh................eeeeeeeee....eeeeeeeeee.hhhhhhh..........eeeee.............eehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------HIS_ACID_PHOSPH----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HIS_ACID_PHOSPHAT------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dkm A   1 QSEPELKLESVVIVSRHGVRAPTKATQLMQDVTPDAWPTWPVKLGWLTPRGGELIAYLGHYQRQRLVADGLLAKKGCPQSGQVAIIADVDERTRKTGEAFAAGLAPDCAITVHTQTDTSSPDPLFNPLKTGVCQLDNANVTDAILSRAGGSIADFTGHRQTAFRELERVLNFPQSNLCLKREKQDESCSLTQALPSELKVSADNVSLTGAVSLASMLTEIFLLQQAQGMPEPGWGRITDSHQWNTLLSLHNAQFYLLQRTPEVARSRATPLLDLIKTALTPHPPQKQAYGVTLPTSVLFIAGHDTNLANLGGALELNWTLPGQPDNTPPGGELVFERWRRLSDNSQWIQVSLVFQTLQQMRDKTPLSLNTPPGEVKLTLAGCEERNAQGMCSLAGFTQIVNEARIPACSL 410
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410

   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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PPA_ECOLI | P07102)
molecular function
    GO:0008707    4-phytase activity    Catalysis of the reaction: myo-inositol hexakisphosphate + H2O = 1-myo-inositol 1,2,3,4,5-pentakisphosphate + phosphate.
    GO:0003993    acid phosphatase activity    Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0071454    cellular response to anoxia    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating a decline in oxygen levels to trace amounts, <0.1%.
    GO:0016036    cellular response to phosphate starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of phosphate.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        PPA_ECOLI | P071021dkl 1dkn 1dko 1dkp 1dkq 4tsr

(-) Related Entries Specified in the PDB File

1dkl PHYTASE AT PH 4.5 (NO LIGAND BOUND)
1dkn PHYTASE AT PH 5.0 (HG2+ ACTING AS AN INTERMOLECULAR BRIDGE)
1dko PHYTASE AT PH 6.6 (TUNGSTATE BOUND AT THE ACTIVE SITE, HG2+ ACTING AS AN INTERMOLECULAR BRIDGE)
1dkp PHYTASE AT PH 6.6 (PHYTATE BOUND IN ACTIVE SITE, HG2+ ACTING AS AN INTERMOLECULAR BRIDGE)
1dkq PHYTASE AT PH 5.0 (PHYTATE BOUND IN ACTIVE SITE, HG2+ ACTING AS AN INTERMOLECULAR BRIDGE)