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(-) Description

Title :  ARPTE (K185R/D208G/N265D/T274N)
 
Authors :  J. L. Foo, C. J. Jackson, P. D. Carr, D. L. Ollis
Date :  07 Jul 09  (Deposition) - 12 Jan 10  (Release) - 12 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Phosphotriesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Jackson, J. -L. Foo, N. Tokuriki, L. Afriat, P. D. Carr, H. -K. Kim, G. Schenk, D. S. Tawfik, D. L. Ollis
Conformational Sampling, Catalysis, And Evolution Of The Bacterial Phosphotriesterase
Proc. Natl. Acad. Sci. Usa 2009
PubMed-ID: 19966226  |  Reference-DOI: 10.1073/PNAS.0907548106
(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: PETMCS1
    Expression System Strain: BL21
    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

 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
2EDO1Ligand/Ion1,2-ETHANEDIOL
3KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
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:668 , CO A:801BINDING SITE FOR RESIDUE CO A 800
2AC2SOFTWAREHOH A:12 , KCX A:169 , HIS A:201 , HIS A:230 , HOH A:668 , CO A:800BINDING SITE FOR RESIDUE CO A 801
3AC3SOFTWARETRP A:131 , SER A:308 , HOH A:420BINDING SITE FOR RESIDUE EDO A 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A4J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3A4J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A4J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3A4J)

(-) Exons   (0, 0)

(no "Exon" information available for 3A4J)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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:328
 aligned with Q93LD7_RHIRD | Q93LD7 from UniProtKB/TrEMBL  Length:384

    Alignment length:328
                                    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        
         Q93LD7_RHIRD    33 GDLINTVRGPIPVSEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRHARSAGVQTIVDVSTFDIGRDVRLLAEVSRAADVHIVAATGLWFDPPLSMRMRSVEELTQFFLREIQHGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTSASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTGLAARGYLVGLDRMPYSAIGLEGNASALALFGTRSWQTRALLIKALIDRGYKDRILVSHDWLFGFSSYVTNIMDVMDRINPDGMAFVPLRVIPFLREKGVPPETLAGVTVANPARFLSPT 360
               SCOP domains d3a4ja_ A: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3a4jA00 A:34-361 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.hhh..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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a4j A  34 GDLINTVRGPIPVSEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRHARAAGVQTIVDVSTFDIGRDVRLLAEVSRAADVHIVAATGLWFDPPLSMRMRSVEELTQFFLREIQHGIEDTGIRAGIIkVATTGKATPFQELVLRAAARASLATGVPVTTHTSASQRGGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTGLAARGYLVGLDRMPYSAIGLEGDASALALFGNRSWQTRALLIKALIDRGYKDRILVSHDWLFGFSSYVTNIMDVMDRINPDGMAFVPLRVIPFLREKGVPPETLAGVTVANPARFLSPT 361
                                    43        53        63        73        83        93       103       113       123       133       143       153       163     | 173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353        
                                                                                                                                                                 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  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A4J)

(-) 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

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

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

(-) Related Entries Specified in the PDB File

2r1n 3a3w 3a3x