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(-) Description

Title :  ORGANOPHOSHATEDEGRADING ENZYME (OPDA)-PHOSPHATE COMPLEX
 
Authors :  F. Ely, M. Pedroso, L. R. Gahan, D. L. Ollis, L. W. Guddat, G. Schenk
Date :  30 Jun 11  (Deposition) - 07 Dec 11  (Release) - 07 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Opda, Phosphotriesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Ely, M. M. Pedroso, L. R. Gahan, D. L. Ollis, L. W. Guddat, G. Schenk
Phosphate-Bound Structure Of An Organophosphate-Degrading Enzyme From Agrobacterium Radiobacter.
J. Inorg. Biochem. V. 106 19 2011
PubMed-ID: 22112835  |  Reference-DOI: 10.1016/J.JINORGBIO.2011.09.015

(-) Compounds

Molecule 1 - PHOSPHOTRIESTERASE
    Chains: A
    Engineered: YES
    Fragment: UNP RESIDUES 32-360
    Gene: OPDA
    Organism Common: AGROBACTERIUM TUMEFACIENS
    Organism Scientific: RHIZOBIUM RADIOBACTER
    Organism Taxid: 358

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1CO2Ligand/IonCOBALT (II) ION
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3NA2Ligand/IonSODIUM ION
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3NA-1Ligand/IonSODIUM ION
4PO42Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:55 , HIS A:57 , KCX A:169 , ASP A:301 , PO4 A:362 , CO A:801BINDING SITE FOR RESIDUE CO A 800
2AC2SOFTWAREKCX A:169 , HIS A:201 , HIS A:230 , PO4 A:362 , CO A:800BINDING SITE FOR RESIDUE CO A 801
3AC3SOFTWARENA A:2 , PO4 A:362BINDING SITE FOR RESIDUE NA A 1
4AC4SOFTWARENA A:1 , TYR A:257 , PO4 A:362BINDING SITE FOR RESIDUE NA A 2
5AC5SOFTWARENA A:1 , NA A:2 , HIS A:55 , HIS A:57 , TRP A:131 , KCX A:169 , HIS A:201 , HIS A:230 , ARG A:254 , ASP A:301 , HOH A:525 , CO A:800 , CO A:801BINDING SITE FOR RESIDUE PO4 A 362

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SO7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SO7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SO7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SO7)

(-) Exons   (0, 0)

(no "Exon" information available for 3SO7)

(-) Sequences/Alignments

Asymmetric Unit
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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: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 d3so7a_ 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.eeeeeee.....hhhhhh.hhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh...hhh.eee.hhhhh.hhhhhhhhhhh..eeee............hhhhhhhhh..hhhhhhhhhhhhhhhhhhh.eee......ee.....hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3so7 A  33 TGDLINTVRGPIPVSEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRHARAAGVQTIVDVSTFDIGRDVRLLAEVSRAADVHIVAATGLWFDPPLSMRMRSVEELTQFFLREIQHGIEDTGIRAGIIkVATTGKATPFQELVLKAAARASLATGVPVTTHTSASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTGLAARGYLVGLDRMPYSAIGLEGNASALALFGTRSWQTRALLIKALIDRGYKDRILVSHDWLFGFSSYVTNIMDVMDRINPDGMAFVPLRVIPFLREKGVPPETLAGVTVANPARFLSPT 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 3SO7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SO7)

(-) 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 3ood 3oqe 3wml 4np7

(-) Related Entries Specified in the PDB File

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