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(-) Description

Title :  STRUCTURE OF AN ENGINEERED ORGANOPHOSPHOROUS HYDROLASE WITH INCREASED ACTIVITY TOWARD HYDROLYSIS OF PHOSPHOTHIOLATE BONDS
 
Authors :  A. D. Mesecar, J. K. Grimsley, T. Holton, J. R. Wild
Date :  01 Sep 03  (Deposition) - 30 Nov 04  (Release) - 30 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Organophosphorous Hydrolase, Phosphotriesterase, Vx, Rvx, 4- Methylbenzylphosphonate, Mutant (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. K. Grimsley, B. Calamini, J. R. Wild, A. D. Mesecar
Structural And Mutational Studies Of Organophosphorus Hydrolase Reveal A Cryptic And Functional Allosteric-Binding Site.
Arch. Biochem. Biophys. V. 442 169 2005
PubMed-ID: 16188223  |  Reference-DOI: 10.1016/J.ABB.2005.08.012
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PARATHION HYDROLASE
    Chains: A, B
    EC Number: 3.1.8.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: OPD
    Mutation: YES
    Organism Scientific: BREVUNDIMONAS DIMINUTA
    Organism Taxid: 293
    Synonym: PHOSPHOTRIESTERASE, PTE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1CO4Ligand/IonCOBALT (II) ION
2EBP2Ligand/IonDIETHYL 4-METHYLBENZYLPHOSPHONATE
3KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4NA2Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREKCX A:169 , HIS A:201 , HIS A:230 , ARG A:254 , CO A:602 , HOH A:802 , HOH A:826BINDING SITE FOR RESIDUE CO A 601
2AC2SOFTWAREHIS A:55 , HIS A:57 , KCX A:169 , ASP A:301 , CO A:601 , HOH A:802BINDING SITE FOR RESIDUE CO A 602
3AC3SOFTWAREHIS B:55 , HIS B:57 , KCX B:169 , ASP B:301 , CO B:604 , HOH B:774BINDING SITE FOR RESIDUE CO B 603
4AC4SOFTWAREKCX B:169 , HIS B:201 , HIS B:230 , ARG B:254 , CO B:603 , HOH B:774 , HOH B:776BINDING SITE FOR RESIDUE CO B 604
5AC5SOFTWAREASN A:38 , ILE A:154 , HOH A:913 , HOH B:719BINDING SITE FOR RESIDUE NA A 605
6AC6SOFTWAREASN B:38 , ILE B:154 , HOH B:802 , HOH B:830BINDING SITE FOR RESIDUE NA B 606
7AC7SOFTWAREGLN A:155 , TYR A:156 , GLU B:71 , THR B:350BINDING SITE FOR RESIDUE EBP B 701
8AC8SOFTWAREPHE A:51 , GLU A:71 , HOH A:969 , GLN B:155 , TYR B:156 , ARG B:164BINDING SITE FOR RESIDUE EBP A 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QW7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QW7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QW7)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHOSPHOTRIESTERASE_2PS51347 Phosphotriesterase family profile.OPD_BREDI35-363
 		  2A:35-363
B:35-363
2PHOSPHOTRIESTERASE_1PS01322 Phosphotriesterase family signature 1.OPD_BREDI50-58
 		  2A:50-58
B:50-58

(-) Exons   (0, 0)

(no "Exon" information available for 1QW7)

(-) 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:336
 aligned with OPD_BREDI | P0A434 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:336
                                    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      
            OPD_BREDI    30 SIGTGDRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRAS 365
               SCOP domains d1qw7a_ A: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1qw7A00 A:30-365 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee...eeee..eeeehhhhh.eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eee.....hhhhhh.hhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhhh..eeee............hhhhhhhhh..hhhhhhhhhhhhhhh.hhh.eee.............hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----PHOSPHOTRIESTERASE_2  PDB: A:35-363 UniProt: 35-363                                                                                                                                                                                                                                                                                      -- PROSITE (1)
                PROSITE (2) --------------------PHOSPHOTR------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qw7 A  30 SIGTGDRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIkVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDRIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRAS 365
                                    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      
                                                                                                                                                                     169-KCX                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:336
 aligned with OPD_BREDI | P0A434 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:336
                                    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      
            OPD_BREDI    30 SIGTGDRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRAS 365
               SCOP domains d1qw7b_ B: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1qw7B00 B:30-365 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) --------------PTE-1qw7B01 B:44-359                                                                                                                                                                                                                                                                                                        ------ Pfam domains (1)
           Pfam domains (2) --------------PTE-1qw7B02 B:44-359                                                                                                                                                                                                                                                                                                        ------ Pfam domains (2)
         Sec.struct. author .ee...eeee..eeeehhhhh.eeeee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eee.....hhhhhh.hhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhhh..eeee............hhhhhhhhh..hhhhhhhhhhhhhhh.hhh.eee......ee.....hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----PHOSPHOTRIESTERASE_2  PDB: B:35-363 UniProt: 35-363                                                                                                                                                                                                                                                                                      -- PROSITE (1)
                PROSITE (2) --------------------PHOSPHOTR------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qw7 B  30 SIGTGDRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIkVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDRIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRAS 365
                                    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      
                                                                                                                                                                     169-KCX
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (OPD_BREDI | P0A434)
molecular function
    GO:0004063    aryldialkylphosphatase activity    Catalysis of the reaction: aryl dialkyl phosphate + H2O = dialkyl phosphate + an aryl alcohol.
    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:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009056    catabolic process    The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  1qw7
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  3.1.8.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        OPD_BREDI | P0A434: 1dpm 1eyw 1ez2 1hzy 1i0b 1i0d 1jgm 1psc 1pta 2o4m 2o4q 2ob3 2oql 3cak 3cs2 3e3h 3upm 3ur2 3ur5 3ura 3urb 3urn 3urq 4e3t 4gy0 4gy1 4zst 4zsu

(-) Related Entries Specified in the PDB File

1dpm THREE-DIMENSIONAL STRUCTURE OF THE ZINC-CONTAINING PHOSPHOTRIESTERASE WITH BOUND SUBSTRATE ANALOG DIETHYL 4- METHYLBENZYLPHOSPHONATE