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(-) Description

Title :  DIISOPROPYL FLUOROPHOSPHATASE (DFPASE), ACTIVE SITE MUTANTS
 
Authors :  J. C. -H. Chen, M. -M. Blum
Date :  27 May 09  (Deposition) - 10 Nov 09  (Release) - 08 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Phosphotriesterase, Beta Propeller, Calcium Binding, Calcium, Hydrolase, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Melzer, J. C. Chen, A. Heidenreich, J. Gab, M. Koller, K. Kehe, M. M. Blum
Reversed Enantioselectivity Of Diisopropyl Fluorophosphatase Against Organophosphorus Nerve Agents By Rational Design
J. Am. Chem. Soc. V. 131 17226 2009
PubMed-ID: 19894712  |  Reference-DOI: 10.1021/JA905444G
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIISOPROPYL-FLUOROPHOSPHATASE
    Chains: A, B, C, D
    EC Number: 3.1.8.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: COMMON EUROPEAN SQUID
    Organism Scientific: LOLIGO VULGARIS
    Organism Taxid: 6622
    Synonym: DFPASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:21 , ASN A:120 , ASN A:175 , ASP A:229 , HOH A:318 , HOH A:319BINDING SITE FOR RESIDUE CA A 315
2AC2SOFTWAREASP A:232 , LEU A:273 , HIS A:274 , HOH A:321 , HOH A:325 , HOH A:328BINDING SITE FOR RESIDUE CA A 316
3AC3SOFTWAREPHE A:314 , GLU B:21 , ASN B:120 , ASN B:175 , ASP B:229 , HOH B:324 , HOH B:369BINDING SITE FOR RESIDUE CA B 315
4AC4SOFTWAREASP B:232 , LEU B:273 , HIS B:274 , HOH B:338 , HOH B:367 , HOH B:378BINDING SITE FOR RESIDUE CA B 316
5AC5SOFTWAREPHE B:314 , GLU C:21 , ASN C:120 , ASN C:175 , ASP C:229 , HOH C:317 , HOH C:320BINDING SITE FOR RESIDUE CA C 315
6AC6SOFTWAREASP C:232 , LEU C:273 , HIS C:274 , HOH C:318 , HOH C:319 , HOH C:330BINDING SITE FOR RESIDUE CA C 316
7AC7SOFTWAREGLU D:21 , ASN D:120 , ASN D:175 , ASP D:229 , HOH D:317 , HOH D:326BINDING SITE FOR RESIDUE CA D 315
8AC8SOFTWAREASP D:232 , LEU D:273 , HIS D:274 , HOH D:318 , HOH D:321 , HOH D:329BINDING SITE FOR RESIDUE CA D 316

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:140 -Pro A:141
2Ala B:140 -Pro B:141
3Ala C:140 -Pro C:141
4Ala D:140 -Pro D:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HLI)

(-) Sequences/Alignments

Asymmetric 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:313
 aligned with DFPA_LOLVU | Q7SIG4 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:313
                                    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   
           DFPA_LOLVU     2 EIPVIEPLFTKVTEDIPGAEGPVFDKNGDFYIVAPEVEVNGKPAGEILRIDLKTGKKTVICKPEVNGYGGIPAGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIAKKDSEGRRMQGCNDCAFDYEGNLWITAPAGEVAPADYTRSMQEKFGSIYCFTTDGQMIQVDTAFQFPNGIAVRHMNDGRPYQLIVAETPTKKLWSYDIKGPAKIENKKVWGHIPGTHEGGADGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPSNLHFKPQTKTIFVTEHENNAVWKFEWQRNGKKQYCETLKFGIF 314
               SCOP domains d3hlia_ A: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 3hliA00 A:2-314 TolB, C-terminal domain                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee......eeeee.....eeeee...ee..ee..eeeee......eeeee..ee..ee..eeeeee.....eeeeee...eeeeee....eee................eee.....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
                 3hli A   2 EIPVIEPLFTKVTEDIPGAEGPVFDKNGDFYIVAPDVEVNGKPAGEILRIDLKTGKKTVICKPEVNGYGGIPAGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIAKKDSEGRRMQGCNDCAFDYEGNLWITAPAGEVAPADATASMQEKFGSIYCFTTDGQMIQVDTAFQFPNGIAVRHMNDGRPYQLIVAEMPTKKLWSYDIKGPAKIENKKVWGHIPGTHEGGADGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPSNLHFKPQTKTIFVTEHENNAVWKFEWQRNGKKQYCETLKFGIF 314
                                    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   


Chain B 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 d3hlib_ B: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3hliB00 B:3-314 TolB, C-terminal domain                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee....eeee......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
                 3hli B   3 IPVIEPLFTKVTEDIPGAEGPVFDKNGDFYIVAPDVEVNGKPAGEILRIDLKTGKKTVICKPEVNGYGGIPAGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIAKKDSEGRRMQGCNDCAFDYEGNLWITAPAGEVAPADATASMQEKFGSIYCFTTDGQMIQVDTAFQFPNGIAVRHMNDGRPYQLIVAEMPTKKLWSYDIKGPAKIENKKVWGHIPGTHEGGADGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPSNLHFKPQTKTIFVTEHENNAVWKFEWQRNGKKQYCETLKFGIF 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  


Chain C 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 d3hlic_ C: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3hliC00 C:3-314 TolB, C-terminal domain                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee....eeee......eeeee.....eeeee...ee..ee..eeeee......eeeee..ee..ee..eeeeee.....eeeeee...eeeeee....eee................eee.....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
                 3hli C   3 IPVIEPLFTKVTEDIPGAEGPVFDKNGDFYIVAPDVEVNGKPAGEILRIDLKTGKKTVICKPEVNGYGGIPAGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIAKKDSEGRRMQGCNDCAFDYEGNLWITAPAGEVAPADATASMQEKFGSIYCFTTDGQMIQVDTAFQFPNGIAVRHMNDGRPYQLIVAEMPTKKLWSYDIKGPAKIENKKVWGHIPGTHEGGADGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPSNLHFKPQTKTIFVTEHENNAVWKFEWQRNGKKQYCETLKFGIF 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  


Chain D 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 d3hlid_ D: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3hliD00 D:3-314 TolB, C-terminal domain                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee....eeee......eeeee.....eeeee...ee..ee..eeeee......eeeee..ee..ee..eeeeee.....eeeeee...eeeeee....eee................eee.....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
                 3hli D   3 IPVIEPLFTKVTEDIPGAEGPVFDKNGDFYIVAPDVEVNGKPAGEILRIDLKTGKKTVICKPEVNGYGGIPAGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIAKKDSEGRRMQGCNDCAFDYEGNLWITAPAGEVAPADATASMQEKFGSIYCFTTDGQMIQVDTAFQFPNGIAVRHMNDGRPYQLIVAEMPTKKLWSYDIKGPAKIENKKVWGHIPGTHEGGADGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPSNLHFKPQTKTIFVTEHENNAVWKFEWQRNGKKQYCETLKFGIF 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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    → 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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1e1a 2gvu 2gvv 2gvw 2gvx 3byc 3hlh