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(-) Description

Title :  OPDA FROM AGROBACTERIUM RADIOBACTER WITH BOUND DIETHYL PHOSPHATE FROM CRYSTAL SOAKING WITH THE COMPOUND- 1.9 A
 
Authors :  D. L. Ollis, C. J. Jackson, J. L. Foo, H. K. Kim, P. D. Carr, J. W. Liu, G. Salem
Date :  23 Aug 07  (Deposition) - 12 Feb 08  (Release) - 23 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Phosphotriesterase, Opda, Metalloenzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Jackson, J. L. Foo, H. K. Kim, P. D. Carr, J. W. Liu, G. Salem, D. L. Ollis
In Crystallo Capture Of A Michaelis Complex And Product-Binding Modes Of A Bacterial Phosphotriesterase
J. Mol. Biol. V. 375 1189 2008
PubMed-ID: 18082180  |  Reference-DOI: 10.1016/J.JMB.2007.10.061
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOTRIESTERASE
    Chains: A
    EC Number: 3.1.8.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCY76
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 32-360
    Gene: OPDA
    Mutation: YES
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 358
    Synonym: PROTEIN OPDA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 5)

Asymmetric Unit (5, 5)
No.NameCountTypeFull Name
1CO1Ligand/IonCOBALT (II) ION
2DPF1Ligand/IonDIETHYL HYDROGEN PHOSPHATE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4FE21Ligand/IonFE (II) ION
5KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2DPF1Ligand/IonDIETHYL HYDROGEN PHOSPHATE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4FE21Ligand/IonFE (II) ION
5KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2DPF2Ligand/IonDIETHYL HYDROGEN PHOSPHATE
3EDO2Ligand/Ion1,2-ETHANEDIOL
4FE22Ligand/IonFE (II) ION
5KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:55 , HIS A:57 , ASP A:301BINDING SITE FOR RESIDUE FE2 A 800
2AC2SOFTWAREHIS A:201 , HIS A:230BINDING SITE FOR RESIDUE CO A 801
3AC3SOFTWAREHIS A:55 , GLY A:60 , TRP A:131 , HIS A:201 , HIS A:230 , ARG A:254 , TYR A:257 , ASP A:301BINDING SITE FOR RESIDUE DPF A 1
4AC4SOFTWARESER A:308 , TYR A:309 , HOH A:1046BINDING SITE FOR RESIDUE EDO A 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R1K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R1K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R1K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R1K)

(-) Exons   (0, 0)

(no "Exon" information available for 2R1K)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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   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: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 d2r1ka_ A: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2r1kA00 A:33-361 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -----------PTE-2r1kA01 A:44-359                                                                                                                                                                                                                                                                                                        -- 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
                 2r1k A  33 TGDLINTVRGPIPVSEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRHARAAGVQTIVDVSTFDIGRDVRLLAEVSRAADVHIVAATGLWFDPPLSMRMRSVEELTQFFLREIQHGIEDTGIRAGIIkVATTGKATPFQELVLKAAARASLATGVPVTTHTSASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTGLAARGYLVGLDRMPYSAIGLEGDASALALFGTRSWQTRALLIKALIDRGYKDRILVSHDWLFGFSSYVTNIMDVMDRINPDGMAFVPLRVIPFLREKGVPPETLAGVTVANPARFLSPT 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
   Legend:   → Mismatch (orange background)
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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  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Amidohydrolase (126)

(-) 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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  2r1k
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  Q93LD7_RHIRD | Q93LD7
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2d2g OPDA WITH BOUND INHIBITOR DIMETHYL PHOSPHATE
2d2h OPDA WITH BOUND INHIBITOR TRIMETHYL PHOSPHATE
2d2j OPDA WITHOUT INHIBITOR/PRODUCT PRESENT
2r1l OPDA WITH BOUND DIETHYL THIOPHOSPHATE FROM CRYSTAL SOAKING WITH THE COMPOUND
2r1m OPDA WITH BOUND PRODUCT DIETHYL PHOSPHATE FROM CRYSTAL SOAKING WITH DIETHYL 4-METHOXYPHENYL PHOSPHATE (450H)
2r1n OPDA WITH BOUND SLOW SUBSTRATE DIETHYL 4-METHOXYPHENYL PHOSPHATE (20H)
2r1o OPDA WITH BOUND DIETHYL THIOPHOSPHATE FROM CRYSTAL SOAKING WITH TETRAETHYL DITHIOPYROPHOSPHATE
2r1p OPDA WITH BOUND DIETHYL THIOPHOSPHATE FROM CO- CRYSTALLISATION WITH TETRAETHYL DITHIOPYROPHOSPHATE