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(-) Description

Title :  STRUCTURE OF PHOSPHOTRIESTERASE MUTANT H254Q/H257F
 
Authors :  J. Kim, P. Tsai, F. M. Raushel, S. C. Almo
Date :  31 Jan 07  (Deposition) - 19 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Metalloenzyme, Tim Barrel, Nerve Agents, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Kim, F. M. Raushel, S. C. Almo
Crystal Structure Of Pte Mutant H254Q/H257F
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PARATHION HYDROLASE
    Chains: A, B
    EC Number: 3.1.8.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    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, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1BTB2Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2GOL3Ligand/IonGLYCEROL
3KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4ZN4Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:55 , HIS A:57 , KCX A:169 , ASP A:301 , GOL A:802 , HOH A:856BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREKCX A:169 , HIS A:201 , HIS A:230 , HOH A:856 , HOH A:988 , HOH A:1098BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWAREHIS B:55 , HIS B:57 , KCX B:169 , ASP B:301 , GOL B:803 , HOH B:1041BINDING SITE FOR RESIDUE ZN B 401
4AC4SOFTWAREKCX B:169 , HIS B:201 , HIS B:230 , HOH B:1027 , HOH B:1038 , HOH B:1041BINDING SITE FOR RESIDUE ZN B 402
5AC5SOFTWAREPHE A:72 , PHE A:73 , THR A:311 , ASP A:315 , HOH A:826 , HOH A:849 , HOH A:934 , HOH A:1074 , HOH A:1086 , HOH A:1139BINDING SITE FOR RESIDUE BTB A 701
6AC6SOFTWAREPHE B:72 , PHE B:73 , THR B:311 , ASP B:315 , HOH B:817 , HOH B:913 , HOH B:976 , HOH B:1074 , HOH B:1096 , HOH B:1116BINDING SITE FOR RESIDUE BTB B 701
7AC7SOFTWAREHIS A:57 , TRP A:131 , KCX A:169 , ASP A:301 , ZN A:401 , HOH A:856 , HOH A:924 , HOH A:980 , HOH A:1098 , HOH A:1104BINDING SITE FOR RESIDUE GOL A 802
8AC8SOFTWAREALA B:63 , GLY B:64 , ARG B:67 , ARG B:108 , ASP B:109 , GLU B:159 , HOH B:818 , HOH B:851 , HOH B:891BINDING SITE FOR RESIDUE GOL B 801
9AC9SOFTWAREHIS B:57 , KCX B:169 , ASP B:301 , ZN B:401 , HOH B:941 , HOH B:1027 , HOH B:1038 , HOH B:1041BINDING SITE FOR RESIDUE GOL B 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OQL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OQL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHOSPHOTRIESTERASE_2PS51347 Phosphotriesterase family profile.OPD_BREDI35-363  1B: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 2OQL)

(-) 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:330
 aligned with OPD_BREDI | P0A434 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:330
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365
            OPD_BREDI    36 RINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRAS 365
               SCOP domains d2oqla_ A: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2oqlA00 A:36-365 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee..eeehhhhhh.eeeee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eee.....hhhhhh.hhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..hhh.eee.......hhhhhhhhhhh..eeee............hhhhhhhhh..hhhhhhhhhhhhhhh.hhh.eee......ee.....hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) PHOSPHOTRIESTERASE_2  PDB: - UniProt: 35-363                                                                                                                                                                                                                                                                                            -- PROSITE (1)
                PROSITE (2) --------------PHOSPHOTR------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2oql A  36 RINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIkVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDQIPFSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRAS 365
                                    45        55        65        75        85        95       105       115       125       135       145       155       165   |   175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365
                                                                                                                                                               169-KCX                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:330
 aligned with OPD_BREDI | P0A434 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:330
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364
            OPD_BREDI    35 DRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRA 364
               SCOP domains d2oqlb_ B: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2oqlB00 B:35-364 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) ---------PTE-2oqlB01 B:44-359                                                                                                                                                                                                                                                                                                        ----- Pfam domains (1)
           Pfam domains (2) ---------PTE-2oqlB02 B:44-359                                                                                                                                                                                                                                                                                                        ----- Pfam domains (2)
         Sec.struct. author ..eee..eeehhhhhh.eeeee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eeee....hhhhhh.hhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhhh..eeee............hhhhhhhhh..hhhhhhhhhhhhhhhhhhh.eee......ee.....hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..... 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
                 2oql B  35 DRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIkVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDQIPFSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRA 364
                                    44        54        64        74        84        94       104       114       124       134       144       154       164    |  174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364
                                                                                                                                                                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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 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 1qw7 2o4m 2o4q 2ob3 3cak 3cs2 3e3h 3upm 3ur2 3ur5 3ura 3urb 3urn 3urq 4e3t 4gy0 4gy1 4zst 4zsu

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