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Protein

2-methylcitrate dehydratase

Gene

prpD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Involved in the catabolism of short chain fatty acids (SCFA) via the tricarboxylic acid (TCA)(acetyl degradation route) and via the 2-methylcitrate cycle I (propionate degradation route). Catalyzes the stereospecific dehydration of (2S,3S)-2-methylcitrate (2-MC) to yield the cis isomer of 2-methyl-aconitate. Could also catalyze the dehydration of citrate and the hydration of cis-aconitate.By similarity

Catalytic activityi

(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate = (Z)-but-2-ene-1,2,3-tricarboxylate + H2O.By similarity
Citrate = isocitrate.By similarity

Pathway: propanoate degradation

This protein is involved in the pathway propanoate degradation, which is part of Organic acid metabolism.By similarity
View all proteins of this organism that are known to be involved in the pathway propanoate degradation and in Organic acid metabolism.

Pathway: tricarboxylic acid cycle

This protein is involved in step 2 of the subpathway that synthesizes isocitrate from oxaloacetate.By similarity
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Citrate synthase 2 (citZ), Citrate synthase 1 (citA)
  2. Aconitate hydratase A (citB), 2-methylcitrate dehydratase (prpD), 2-methylcitrate synthase (mmgD)
This subpathway is part of the pathway tricarboxylic acid cycle, which is itself part of Carbohydrate metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes isocitrate from oxaloacetate, the pathway tricarboxylic acid cycle and in Carbohydrate metabolism.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Sporulation, Tricarboxylic acid cycle

Enzyme and pathway databases

BioCyciBSUB:BSU24130-MONOMER.
UniPathwayiUPA00223; UER00718.
UPA00946.

Names & Taxonomyi

Protein namesi
Recommended name:
2-methylcitrate dehydrataseBy similarity (EC:4.2.1.79By similarity)
Short name:
2-MC dehydrataseBy similarity
Alternative name(s):
(2S,3S)-2-methylcitrate dehydrataseBy similarity
Probable aconitate hydrataseBy similarity (EC:4.2.1.3By similarity)
Short name:
ACNBy similarity
Short name:
AconitaseBy similarity
Gene namesi
Name:prpD
Synonyms:mmgE, yqiP
Ordered Locus Names:BSU24130
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570 Componenti: Chromosome

Organism-specific databases

GenoListiBSU24130. [Micado]

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 4724722-methylcitrate dehydratasePRO_0000215020Add
BLAST

Proteomic databases

PaxDbiP45859.

Expressioni

Developmental stagei

Expressed in the mother cell at intermediate stages of sporulation under the control of the sigma-E factor.1 Publication

Inductioni

Subject to catabolite repression.1 Publication

Interactioni

Subunit structurei

Monomer.By similarity

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100013231.

Structurei

3D structure databases

ProteinModelPortaliP45859.
SMRiP45859. Positions 5-472.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the PrpD family.Curated

Phylogenomic databases

eggNOGiCOG2079.
HOGENOMiHOG000159916.
InParanoidiP45859.
KOiK01720.
OMAiCLMDTLG.
OrthoDBiEOG6RC3K5.
PhylomeDBiP45859.

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.

P45859-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPKTDRVIEE ITDYVLEKEI TSAEAYTTAG HVLLDTLGCG ILALRYPECT
60 70 80 90 100
KLLGPIVPGT TVPNGSKVPG TSYVLDPVRA AFNIGCMIRW LDYNDTWLAA
110 120 130 140 150
EWGHPSDNLG GILAAADYVS RVRLSEGKEP LTVRDVLEMM IKAHEIQGVL
160 170 180 190 200
ALENSLNRVG LDHVLFVKVA TTAVAAKLLG GGREEIKNAL SNAWIDNAAL
210 220 230 240 250
RTYRHSPNTG SRKSWAAGDA TSRGVHLALM SLKGEMGYPT ALSAPGWGFQ
260 270 280 290 300
DVLFNKKEIK LARPLDAYVM ENVLFKVSYP AEFHAQTAAE SAVILHPQVK
310 320 330 340 350
NRIDEIDRVV IRTHESAIRI IDKKGPLHNP ADRDHCLQYI TAIGLLFGDI
360 370 380 390 400
TAQHYEAETA NDPRIDKLRD KMEVTENKTY TEDYLKPDKR SISNAVQVHF
410 420 430 440 450
KDGTSTEMVE CEFPLGHRFR REEAVPKLLE KFSDNLKTHF PDKQHKHIYE
460 470
RCTSYETLQT MRVNEFVDMF CM
Length:472
Mass (Da):52,878
Last modified:July 7, 2009 - v3
Checksum:i5941EA6EC1DA2142
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti216 – 2161A → P in BAA12591 (PubMed:8969508).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D84432 Genomic DNA. Translation: BAA12591.1.
AL009126 Genomic DNA. Translation: CAB14344.2.
U29084 Genomic DNA. Translation: AAB09617.1.
PIRiF69658.
RefSeqiNP_390293.2. NC_000964.3.
WP_004398686.1. NC_000964.3.

Genome annotation databases

EnsemblBacteriaiCAB14344; CAB14344; BSU24130.
GeneIDi938663.
KEGGibsu:BSU24130.
PATRICi18976654. VBIBacSub10457_2517.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D84432 Genomic DNA. Translation: BAA12591.1.
AL009126 Genomic DNA. Translation: CAB14344.2.
U29084 Genomic DNA. Translation: AAB09617.1.
PIRiF69658.
RefSeqiNP_390293.2. NC_000964.3.
WP_004398686.1. NC_000964.3.

3D structure databases

ProteinModelPortaliP45859.
SMRiP45859. Positions 5-472.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100013231.

Proteomic databases

PaxDbiP45859.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB14344; CAB14344; BSU24130.
GeneIDi938663.
KEGGibsu:BSU24130.
PATRICi18976654. VBIBacSub10457_2517.

Organism-specific databases

GenoListiBSU24130. [Micado]

Phylogenomic databases

eggNOGiCOG2079.
HOGENOMiHOG000159916.
InParanoidiP45859.
KOiK01720.
OMAiCLMDTLG.
OrthoDBiEOG6RC3K5.
PhylomeDBiP45859.

Enzyme and pathway databases

UniPathwayiUPA00223; UER00718.
UPA00946.
BioCyciBSUB:BSU24130-MONOMER.

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. "Systematic sequencing of the 283 kb 210 degrees-232 degrees region of the Bacillus subtilis genome containing the skin element and many sporulation genes."
    Mizuno M., Masuda S., Takemaru K., Hosono S., Sato T., Takeuchi M., Kobayashi Y.
    Microbiology 142:3103-3111(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / JH642.
  2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  3. "From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later."
    Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A., Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.
    Microbiology 155:1758-1775(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: SEQUENCE REVISION TO 216.
  4. "A sigma E dependent operon subject to catabolite repression during sporulation in Bacillus subtilis."
    Bryan E.M., Beall B.W., Moran C.P. Jr.
    J. Bacteriol. 178:4778-4786(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-178, DEVELOPMENTAL STAGE, INDUCTION.
    Strain: 168 / MB24.

Entry informationi

Entry nameiPRPD_BACSU
AccessioniPrimary (citable) accession number: P45859
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: July 7, 2009
Last modified: June 24, 2015
This is version 100 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

Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. 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.