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Protein

2-methylcitrate dehydratase

Gene

prpD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the dehydration of 2-methylcitrate to 2-methyl-cis-aconitate. Also seems to be responsible for the residual aconitase activity of the acnAB-null strain.

Catalytic activityi

(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate = (Z)-but-2-ene-1,2,3-tricarboxylate + H2O.1 Publication

Cofactori

[2Fe-2S] clusterNote: Binds 1 [2Fe-2S] cluster.

Kineticsi

  1. KM=0.44 mM for (2S,3S)-2-methylcitrate1 Publication

Pathwayi

GO - Molecular functioni

  1. 2 iron, 2 sulfur cluster binding Source: UniProtKB-KW
  2. 2-methylcitrate dehydratase activity Source: EcoCyc
  3. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. propionate catabolic process, 2-methylcitrate cycle Source: InterPro
  2. propionate metabolic process, methylcitrate cycle Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

2Fe-2S, Iron, Iron-sulfur, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G6199-MONOMER.
ECOL316407:JW0325-MONOMER.
MetaCyc:G6199-MONOMER.
BRENDAi4.2.1.79. 2026.
SABIO-RKP77243.
UniPathwayiUPA00946.

Names & Taxonomyi

Protein namesi
Recommended name:
2-methylcitrate dehydratase (EC:4.2.1.79)
Gene namesi
Name:prpD
Synonyms:yahT
Ordered Locus Names:b0334, JW0325
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13603. prpD.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 4834822-methylcitrate dehydratasePRO_0000215023Add
BLAST

Proteomic databases

PRIDEiP77243.

Expressioni

Gene expression databases

GenevestigatoriP77243.

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

DIPiDIP-10580N.
IntActiP77243. 4 interactions.
MINTiMINT-1309441.
STRINGi511145.b0334.

Structurei

Secondary structure

1
483
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi14 – 2512Combined sources
Helixi31 – 5121Combined sources
Helixi55 – 584Combined sources
Helixi85 – 9814Combined sources
Beta strandi107 – 1093Combined sources
Helixi113 – 1164Combined sources
Helixi117 – 13317Combined sources
Helixi141 – 15818Combined sources
Turni159 – 1613Combined sources
Helixi165 – 1673Combined sources
Helixi172 – 18615Combined sources
Helixi191 – 20212Combined sources
Helixi210 – 2123Combined sources
Helixi220 – 24021Combined sources
Turni247 – 2515Combined sources
Turni253 – 2553Combined sources
Helixi257 – 2615Combined sources
Beta strandi273 – 2753Combined sources
Helixi276 – 2805Combined sources
Beta strandi286 – 2883Combined sources
Turni291 – 2933Combined sources
Helixi294 – 30916Combined sources
Helixi314 – 3163Combined sources
Beta strandi317 – 3248Combined sources
Helixi326 – 3327Combined sources
Helixi341 – 3444Combined sources
Helixi348 – 35811Combined sources
Helixi363 – 3664Combined sources
Helixi368 – 3714Combined sources
Helixi374 – 3818Combined sources
Beta strandi383 – 3875Combined sources
Helixi389 – 3968Combined sources
Turni398 – 4003Combined sources
Beta strandi405 – 4117Combined sources
Beta strandi420 – 4223Combined sources
Helixi429 – 4313Combined sources
Helixi432 – 45019Combined sources
Helixi453 – 46412Combined sources
Helixi466 – 4716Combined sources
Helixi474 – 4785Combined sources
Turni479 – 4813Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1SZQX-ray2.70A/B1-483[»]
SMRiP77243. Positions 11-483.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP77243.

Family & Domainsi

Sequence similaritiesi

Belongs to the PrpD family.Curated

Phylogenomic databases

eggNOGiCOG2079.
HOGENOMiHOG000159916.
InParanoidiP77243.
KOiK01720.
OMAiCLMDTLG.
OrthoDBiEOG6RC3K5.
PhylomeDBiP77243.

Family and domain databases

InterProiIPR012705. 2Me_IsoCit_deHydtase_PrpD.
IPR005656. MmgE_PrpD.
[Graphical view]
PANTHERiPTHR16943. PTHR16943. 1 hit.
PfamiPF03972. MmgE_PrpD. 1 hit.
[Graphical view]
SUPFAMiSSF103378. SSF103378. 1 hit.
TIGRFAMsiTIGR02330. prpD. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P77243-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSAQINNIRP EFDREIVDIV DYVMNYEISS KVAYDTAHYC LLDTLGCGLE
60 70 80 90 100
ALEYPACKKL LGPIVPGTVV PNGVRVPGTQ FQLDPVQAAF NIGAMIRWLD
110 120 130 140 150
FNDTWLAAEW GHPSDNLGGI LATADWLSRN AVASGKAPLT MKQVLTAMIK
160 170 180 190 200
AHEIQGCIAL ENSFNRVGLD HVLLVKVAST AVVAEMLGLT REEILNAVSL
210 220 230 240 250
AWVDGQSLRT YRHAPNTGTR KSWAAGDATS RAVRLALMAK TGEMGYPSAL
260 270 280 290 300
TAPVWGFYDV SFKGESFRFQ RPYGSYVMEN VLFKISFPAE FHSQTAVEAA
310 320 330 340 350
MTLYEQMQAA GKTAADIEKV TIRTHEACIR IIDKKGPLNN PADRDHCIQY
360 370 380 390 400
MVAIPLLFGR LTAADYEDNV AQDKRIDALR EKINCFEDPA FTADYHDPEK
410 420 430 440 450
RAIANAITLE FTDGTRFEEV VVEYPIGHAR RRQDGIPKLV DKFKINLARQ
460 470 480
FPTRQQQRIL EVSLDRARLE QMPVNEYLDL YVI
Length:483
Mass (Da):53,952
Last modified:January 23, 2007 - v3
Checksum:i965252C8983E6F64
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U73857 Genomic DNA. Translation: AAB18058.1.
U00096 Genomic DNA. Translation: AAC73437.1.
AP009048 Genomic DNA. Translation: BAE76116.1.
PIRiF64760.
RefSeqiNP_414868.1. NC_000913.3.
YP_488628.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73437; AAC73437; b0334.
BAE76116; BAE76116; BAE76116.
GeneIDi12930816.
945931.
KEGGiecj:Y75_p0323.
eco:b0334.
PATRICi32115799. VBIEscCol129921_0341.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U73857 Genomic DNA. Translation: AAB18058.1.
U00096 Genomic DNA. Translation: AAC73437.1.
AP009048 Genomic DNA. Translation: BAE76116.1.
PIRiF64760.
RefSeqiNP_414868.1. NC_000913.3.
YP_488628.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1SZQX-ray2.70A/B1-483[»]
SMRiP77243. Positions 11-483.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-10580N.
IntActiP77243. 4 interactions.
MINTiMINT-1309441.
STRINGi511145.b0334.

Proteomic databases

PRIDEiP77243.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73437; AAC73437; b0334.
BAE76116; BAE76116; BAE76116.
GeneIDi12930816.
945931.
KEGGiecj:Y75_p0323.
eco:b0334.
PATRICi32115799. VBIEscCol129921_0341.

Organism-specific databases

EchoBASEiEB3371.
EcoGeneiEG13603. prpD.

Phylogenomic databases

eggNOGiCOG2079.
HOGENOMiHOG000159916.
InParanoidiP77243.
KOiK01720.
OMAiCLMDTLG.
OrthoDBiEOG6RC3K5.
PhylomeDBiP77243.

Enzyme and pathway databases

UniPathwayiUPA00946.
BioCyciEcoCyc:G6199-MONOMER.
ECOL316407:JW0325-MONOMER.
MetaCyc:G6199-MONOMER.
BRENDAi4.2.1.79. 2026.
SABIO-RKP77243.

Miscellaneous databases

EvolutionaryTraceiP77243.
PROiP77243.

Gene expression databases

GenevestigatoriP77243.

Family and domain databases

InterProiIPR012705. 2Me_IsoCit_deHydtase_PrpD.
IPR005656. MmgE_PrpD.
[Graphical view]
PANTHERiPTHR16943. PTHR16943. 1 hit.
PfamiPF03972. MmgE_PrpD. 1 hit.
[Graphical view]
SUPFAMiSSF103378. SSF103378. 1 hit.
TIGRFAMsiTIGR02330. prpD. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence of minutes 4-25 of Escherichia coli."
    Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
    Submitted (DEC-1996) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "AcnC of Escherichia coli is a 2-methylcitrate dehydratase (PrpD) that can use citrate and isocitrate as substrates."
    Blank L., Green J., Guest J.R.
    Microbiology 148:133-146(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-13, CHARACTERIZATION.
  5. "Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase."
    Brock M., Maerker C., Schuetz A., Voelker U., Buckel W.
    Eur. J. Biochem. 269:6184-6194(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES.
  6. "Crystal structure of 2-methylcitrate dehydratase."
    New York structural genomix research consortium (NYSGXRC)
    Submitted (JAN-2009) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).

Entry informationi

Entry nameiPRPD_ECOLI
AccessioniPrimary (citable) accession number: P77243
Secondary accession number(s): Q2MC90
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 23, 2007
Last modified: April 1, 2015
This is version 126 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.