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Protein
Submitted name:

Phosphotriesterase

Gene

opdA

Organism
Rhizobium radiobacter (Agrobacterium tumefaciens) (Agrobacterium radiobacter)
Status
Unreviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

Cofactori

a divalent metal cationUniRule annotationNote: Binds 2 divalent metal cations per subunit.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi54 – 541Divalent metal cation 1; via tele nitrogenUniRule annotation
Metal bindingi54 – 541Iron; via pros nitrogenCombined sources
Metal bindingi56 – 561Divalent metal cation 1; via tele nitrogenUniRule annotation
Metal bindingi56 – 561Iron; via tele nitrogenCombined sources
Metal bindingi168 – 1681Divalent metal cation 1; via carbamate groupUniRule annotation
Metal bindingi168 – 1681Divalent metal cation 2; via carbamate groupUniRule annotation
Metal bindingi168 – 1681IronCombined sources
Metal bindingi200 – 2001Divalent metal cation 2; via pros nitrogenUniRule annotation
Metal bindingi229 – 2291Divalent metal cation 2; via tele nitrogenUniRule annotation
Metal bindingi300 – 3001Divalent metal cation 1UniRule annotation
Metal bindingi300 – 3001IronCombined sources

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

IronCombined sources, Metal-bindingUniRule annotationCombined sources

Enzyme and pathway databases

BRENDAi3.1.8.1. 200.

Names & Taxonomyi

Protein namesi
Submitted name:
PhosphotriesteraseImported
Gene namesi
Name:opdAImported
OrganismiRhizobium radiobacter (Agrobacterium tumefaciens) (Agrobacterium radiobacter)Imported
Taxonomic identifieri358 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeRhizobium/Agrobacterium groupAgrobacteriumAgrobacterium tumefaciens complex

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2727Sequence analysisAdd
BLAST
Chaini28 – 384357Sequence analysisPRO_5004320068Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei168 – 1681N6-carboxylysineUniRule annotation

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2D2GX-ray1.85A32-360[»]
2D2HX-ray1.80A32-360[»]
2D2JX-ray1.75A32-360[»]
2R1KX-ray2.10A32-360[»]
2R1LX-ray1.95A32-360[»]
2R1MX-ray2.50A33-360[»]
2R1NX-ray1.70A33-360[»]
2R1PX-ray1.80A33-360[»]
3A3WX-ray1.85A32-360[»]
3A3XX-ray1.70A35-360[»]
3A4JX-ray1.25A32-360[»]
3C86X-ray1.80A33-360[»]
3OODX-ray1.89A32-360[»]
3OQEX-ray1.90A32-360[»]
3SO7X-ray2.20A32-360[»]
3WMLX-ray1.99A32-360[»]
4NP7X-ray1.99A32-360[»]
ProteinModelPortaliQ93LD7.
SMRiQ93LD7. Positions 32-360.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ93LD7.

Family & Domainsi

Keywords - Domaini

SignalSequence analysis

Family and domain databases

InterProiIPR017947. AryldialkylPase_Zn-BS.
IPR032466. Metal_Hydrolase.
IPR001559. Phosphotriesterase.
IPR006311. TAT_signal.
[Graphical view]
PANTHERiPTHR10819. PTHR10819. 1 hit.
PfamiPF02126. PTE. 1 hit.
[Graphical view]
SUPFAMiSSF51556. SSF51556. 1 hit.
PROSITEiPS01322. PHOSPHOTRIESTERASE_1. 1 hit.
PS51347. PHOSPHOTRIESTERASE_2. 1 hit.
PS51318. TAT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q93LD7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQTRRDALKS AAAITLLGGL AGCASMARPI GTGDLINTVR GPIPVSEAGF
60 70 80 90 100
TLTHEHICGS SAGFLRAWPE FFGSRKALAE KAVRGLRHAR SAGVQTIVDV
110 120 130 140 150
STFDIGRDVR LLAEVSRAAD VHIVAATGLW FDPPLSMRMR SVEELTQFFL
160 170 180 190 200
REIQHGIEDT GIRAGIIKVA TTGKATPFQE LVLKAAARAS LATGVPVTTH
210 220 230 240 250
TSASQRDGEQ QAAIFESEGL SPSRVCIGHS DDTDDLSYLT GLAARGYLVG
260 270 280 290 300
LDRMPYSAIG LEGNASALAL FGTRSWQTRA LLIKALIDRG YKDRILVSHD
310 320 330 340 350
WLFGFSSYVT NIMDVMDRIN PDGMAFVPLR VIPFLREKGV PPETLAGVTV
360 370 380
ANPARFLSPT VRAVVTRSET SRPAAPIPRQ DTER
Length:384
Mass (Da):41,363
Last modified:December 1, 2001 - v1
Checksum:i1128E3F2D7AF51B4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY043245 Genomic DNA. Translation: AAK85308.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY043245 Genomic DNA. Translation: AAK85308.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2D2GX-ray1.85A32-360[»]
2D2HX-ray1.80A32-360[»]
2D2JX-ray1.75A32-360[»]
2R1KX-ray2.10A32-360[»]
2R1LX-ray1.95A32-360[»]
2R1MX-ray2.50A33-360[»]
2R1NX-ray1.70A33-360[»]
2R1PX-ray1.80A33-360[»]
3A3WX-ray1.85A32-360[»]
3A3XX-ray1.70A35-360[»]
3A4JX-ray1.25A32-360[»]
3C86X-ray1.80A33-360[»]
3OODX-ray1.89A32-360[»]
3OQEX-ray1.90A32-360[»]
3SO7X-ray2.20A32-360[»]
3WMLX-ray1.99A32-360[»]
4NP7X-ray1.99A32-360[»]
ProteinModelPortaliQ93LD7.
SMRiQ93LD7. Positions 32-360.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi3.1.8.1. 200.

Miscellaneous databases

EvolutionaryTraceiQ93LD7.

Family and domain databases

InterProiIPR017947. AryldialkylPase_Zn-BS.
IPR032466. Metal_Hydrolase.
IPR001559. Phosphotriesterase.
IPR006311. TAT_signal.
[Graphical view]
PANTHERiPTHR10819. PTHR10819. 1 hit.
PfamiPF02126. PTE. 1 hit.
[Graphical view]
SUPFAMiSSF51556. SSF51556. 1 hit.
PROSITEiPS01322. PHOSPHOTRIESTERASE_1. 1 hit.
PS51347. PHOSPHOTRIESTERASE_2. 1 hit.
PS51318. TAT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Identification of an opd (organophosphate degradation) gene in an Agrobacterium isolate."
    Horne I., Sutherland T.D., Harcourt R.L., Russell R.J., Oakeshott J.G.
    Appl. Environ. Microbiol. 68:3371-3376(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: P230Imported.
  2. "The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism."
    Jackson C., Kim H.K., Carr P.D., Liu J.W., Ollis D.L.
    Biochim. Biophys. Acta 1752:56-64(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 32-360.
  3. "In crystallo capture of a Michaelis complex and product-binding modes of a bacterial phosphotriesterase."
    Jackson C.J., Foo J.L., Kim H.K., Carr P.D., Liu J.W., Salem G., Ollis D.L.
    J. Mol. Biol. 375:1189-1196(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 33-360 IN COMPLEX WITH IRON.
  4. "Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase."
    Jackson C.J., Foo J.L., Tokuriki N., Afriat L., Carr P.D., Kim H.K., Schenk G., Tawfik D.S., Ollis D.L.
    Proc. Natl. Acad. Sci. U.S.A. 106:21631-21636(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.25 ANGSTROMS) OF 32-360.
  5. "The organophosphate-degrading enzyme from Agrobacterium radiobacter displays mechanistic flexibility for catalysis."
    Ely F., Hadler K.S., Gahan L.R., Guddat L.W., Ollis D.L., Schenk G.
    Biochem. J. 432:565-573(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.89 ANGSTROMS) OF 32-360.
  6. "Phosphate-bound structure of an organophosphate-degrading enzyme from Agrobacterium radiobacter."
    Ely F., Pedroso M.M., Gahan L.R., Ollis D.L., Guddat L.W., Schenk G.
    J. Inorg. Biochem. 106:19-22(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 32-360.
  7. "A 5000-fold increase in the specificity of a bacterial phosphotriesterase for malathion through combinatorial active site mutagenesis."
    Naqvi T., Warden A.C., French N., Sugrue E., Carr P.D., Jackson C.J., Scott C.
    PLoS ONE 9:e94177-e94177(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.99 ANGSTROMS) OF 32-360 IN COMPLEX WITH IRON.

Entry informationi

Entry nameiQ93LD7_RHIRD
AccessioniPrimary (citable) accession number: Q93LD7
Entry historyi
Integrated into UniProtKB/TrEMBL: December 1, 2001
Last sequence update: December 1, 2001
Last modified: April 13, 2016
This is version 68 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.