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(-) Description

Title :  STRUCTURE OF OPDA Y257F MUTANT SOAKED WITH DIETHYL 4-METHOXYPHENYL PHOSPHATE FOR 20 HOURS.
 
Authors :  F. Ely, L. W. Guddat, D. L. Ollis, G. Schenk
Date :  31 Aug 10  (Deposition) - 02 Nov 11  (Release) - 09 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Binuclear Metallohydrolase, Organophosphate Hydrolysis, Diethyl 4- Methoxyphenyl Phosphate, Bioremediation, Tim Barrel, Phosphotriesterase, Binuclear Metal Ion Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Ely, K. S. Hadler, L. R. Gahan, L. W. Guddat, D. L. Ollis, G. Schenk
The Organophosphate-Degrading Enzyme From Agrobacterium Radiobacter Displays Mechanistic Flexibility For Catalysis.
Biochem. J. V. 432 565 2010
PubMed-ID: 20868365  |  Reference-DOI: 10.1042/BJ20101054

(-) Compounds

Molecule 1 - PHOSPHOTRIESTERASE
    Chains: A
    EC Number: 3.1.8.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETMCSI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 32-360
    Gene: OPDA
    Mutation: YES
    Organism Common: AGROBACTERIUM TUMEFACIENS
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 358
    Synonym: OPDA

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CO2Ligand/IonCOBALT (II) ION
2EPL1Ligand/IonDIETHYL 4-METHOXYPHENYL PHOSPHATE
3KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2EPL2Ligand/IonDIETHYL 4-METHOXYPHENYL PHOSPHATE
3KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:55 , HIS A:57 , KCX A:169 , ASP A:301 , HOH A:434 , HOH A:500 , EPL A:702BINDING SITE FOR RESIDUE CO A 800
2AC2SOFTWAREKCX A:169 , HIS A:201 , HIS A:230 , ARG A:254 , HOH A:500 , EPL A:702BINDING SITE FOR RESIDUE CO A 801
3AC3SOFTWAREHIS A:55 , HIS A:57 , ILE A:106 , TRP A:131 , MET A:140 , KCX A:169 , HIS A:201 , ARG A:254 , PHE A:257 , LEU A:271 , ASP A:301 , PHE A:306 , SER A:308 , TYR A:309 , HOH A:434 , HOH A:435 , HOH A:500 , HOH A:515 , HOH A:602 , CO A:800 , CO A:801BINDING SITE FOR RESIDUE EPL A 702

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:PROTEIN  Length:329
 aligned with Q93LD7_RHIRD | Q93LD7 from UniProtKB/TrEMBL  Length:384

    Alignment length:329
                                    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       321       331       341       351         
         Q93LD7_RHIRD    32 TGDLINTVRGPIPVSEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRHARSAGVQTIVDVSTFDIGRDVRLLAEVSRAADVHIVAATGLWFDPPLSMRMRSVEELTQFFLREIQHGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTSASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTGLAARGYLVGLDRMPYSAIGLEGNASALALFGTRSWQTRALLIKALIDRGYKDRILVSHDWLFGFSSYVTNIMDVMDRINPDGMAFVPLRVIPFLREKGVPPETLAGVTVANPARFLSPT 360
               SCOP domains d3ooda_ A: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.hhh..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.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ood A  33 TGDLINTVRGPIPVSEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRHARSAGVQTIVDVSTFDIGRDVRLLAEVSRAADVHIVAATGLWFDPPLSMRMRSVEELTQFFLREIQHGIEDTGIRAGIIkVATTGKATPFQELVLKAAARASLATGVPVTTHTSASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTGLAARGYLVGLDRMPFSAIGLEGNASALALFGTRSWQTRALLIKALIDRGYKDRILVSHDWLFGFSSYVTNIMDVMDRINPDGMAFVPLRVIPFLREKGVPPETLAGVTVANPARFLSPT 361
                                    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         
                                                                                                                                                                  169-KCX
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  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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OOD)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q93LD7_RHIRD | Q93LD7)
molecular function
    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.

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 Related Entries

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UniProtKB/TrEMBL
        Q93LD7_RHIRD | Q93LD7: 2d2g 2d2h 2d2j 2r1k 2r1l 2r1m 2r1n 2r1p 3a3w 3a3x 3a4j 3c86 3oqe 3so7 3wml 4np7

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