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(-) Description

Title :  CRYSTAL STRUCTURE OF DIISOPROPYL FLUOROPHOSPHATASE (DFPASE), MUTANT D229N / N120D
 
Authors :  J. C. H. Chen, M. M. Blum
Date :  03 May 06  (Deposition) - 19 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphotriesterase, Beta-Propeller, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Blum, F. Lohr, A. Richardt, H. Ruterjans, J. C. Chen
Binding Of A Designed Substrate Analogue To Diisopropyl Fluorophosphatase: Implications For The Phosphotriesterase Mechanism.
J. Am. Chem. Soc. V. 128 12750 2006
PubMed-ID: 17002369  |  Reference-DOI: 10.1021/JA061887N
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOTRIESTERASE
    Chains: A
    EC Number: 3.1.8.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: LOLIGO VULGARIS
    Organism Taxid: 6622
    Synonym: DIISOPROPYL PHOSPHATASE, DFPASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:21 , ASP A:120 , ASN A:175 , ASN A:229 , HOH A:523 , HOH A:524 , HOH A:578BINDING SITE FOR RESIDUE CA A 500
2AC2SOFTWAREASP A:232 , LEU A:273 , HIS A:274 , HOH A:527 , HOH A:555 , HOH A:613BINDING SITE FOR RESIDUE CA A 501

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:78 -A:306

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:140 -Pro A:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GVU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GVU)

(-) Exons   (0, 0)

(no "Exon" information available for 2GVU)

(-) 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:312
 aligned with DFPA_LOLVU | Q7SIG4 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:312
                                    12        22        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  
           DFPA_LOLVU     3 IPVIEPLFTKVTEDIPGAEGPVFDKNGDFYIVAPEVEVNGKPAGEILRIDLKTGKKTVICKPEVNGYGGIPAGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIAKKDSEGRRMQGCNDCAFDYEGNLWITAPAGEVAPADYTRSMQEKFGSIYCFTTDGQMIQVDTAFQFPNGIAVRHMNDGRPYQLIVAETPTKKLWSYDIKGPAKIENKKVWGHIPGTHEGGADGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPSNLHFKPQTKTIFVTEHENNAVWKFEWQRNGKKQYCETLKFGIF 314
               SCOP domains d2gvua_ A: Diisopropylfluorophosphatase (phosphotriesterase, DFP)                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2gvuA00 A:3-314 TolB, C-terminal domain                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee....eeeee.....eeeee.....eeeee...ee..ee..eeeee......eeeee..ee..ee..eeeeee.....eeeeee...eeeeee....eee...............eeee.....eeeee..................eeeeee.....eeeeeeee..eeeeeeee.....eeeeeeee....eeeeeeeee..eeeeeeeeee.......eeeeeee.....eeeeee...eeeee........eeee.....eeeeee.....eeeeee....eeeeee.......hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gvu A   3 IPVIEPLFTKVTEDIPGAEGPVFDKNGDFYIVAPEVEVNGKPAGEILRIDLKTGKKTVICKPEVNGYGGIPAGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIAKKDSEGRRMQGCDDCAFDYEGNLWITAPAGEVAPADYTRSMQEKFGSIYCFTTDGQMIQVDTAFQFPNGIAVRHMNDGRPYQLIVAETPTKKLWSYDIKGPAKIENKKVWGHIPGTHEGGANGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPSNLHFKPQTKTIFVTEHENNAVWKFEWQRNGKKQYCETLKFGIF 314
                                    12        22        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
   Legend:   → Mismatch (orange background)
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  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 2GVU)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DFPA_LOLVU | Q7SIG4)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0047862    diisopropyl-fluorophosphatase activity    Catalysis of the reaction: diisopropyl fluorophosphate + H(2)O = diisopropyl phosphate + 2 H(+) + hydrogen fluoride.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.

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  3.1.8.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        DFPA_LOLVU | Q7SIG4: 1e1a 1pjx 2gvv 2gvw 2gvx 2iao 2iap 2iaq 2iar 2ias 2iat 2iau 2iav 2iaw 2iax 3byc 3hlh 3hli 3i1c 3kgg 3li3 3li4 3li5 3o4p 3u0s 4o5s 4o5t

(-) Related Entries Specified in the PDB File

2gvv STRUCTURE OF DIISOPROPYL FLUOROPHOSPHATASE IN COMPLEX WITH DICYCLOPENTYLPHOSPHOROAMIDATE (DCPPA)
2gvw STRUCTURE OF DIISOPROPYL FLUOROPHOSPHATASE HOLOENZYME (RT)