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Protein

2-methylcitrate dehydratase

Gene

prpD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: -Experimental evidence at protein 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

Pathwayi: 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.

Pathwayi: 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. 2-methylcitrate dehydratase (prpD), Aconitate hydratase A (citB), 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

Keywordsi

Molecular functionLyase
Biological processSporulation, 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
Proteomesi
  • UP000001570 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002150201 – 4722-methylcitrate dehydrataseAdd BLAST472

Proteomic databases

PaxDbiP45859
PRIDEiP45859

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

Secondary structure

1472
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 17Combined sources12
Helixi23 – 43Combined sources21
Helixi47 – 50Combined sources4
Helixi77 – 89Combined sources13
Beta strandi96 – 103Combined sources8
Helixi105 – 108Combined sources4
Helixi109 – 125Combined sources17
Helixi133 – 153Combined sources21
Helixi157 – 159Combined sources3
Helixi164 – 178Combined sources15
Helixi183 – 195Combined sources13
Helixi202 – 204Combined sources3
Turni206 – 208Combined sources3
Helixi211 – 213Combined sources3
Helixi216 – 232Combined sources17
Turni239 – 243Combined sources5
Turni245 – 247Combined sources3
Helixi249 – 253Combined sources5
Beta strandi265 – 267Combined sources3
Helixi268 – 271Combined sources4
Helixi283 – 285Combined sources3
Helixi286 – 299Combined sources14
Beta strandi308 – 313Combined sources6
Helixi315 – 320Combined sources6
Helixi330 – 334Combined sources5
Helixi337 – 347Combined sources11
Helixi352 – 355Combined sources4
Helixi357 – 360Combined sources4
Helixi363 – 369Combined sources7
Beta strandi372 – 376Combined sources5
Helixi378 – 385Combined sources8
Turni387 – 389Combined sources3
Beta strandi394 – 399Combined sources6
Beta strandi409 – 413Combined sources5
Helixi418 – 420Combined sources3
Helixi421 – 437Combined sources17
Helixi442 – 453Combined sources12
Helixi455 – 458Combined sources4
Helixi463 – 466Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5MUXX-ray2.00A/B/C/D/E/F1-472[»]
ProteinModelPortaliP45859
SMRiP45859
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the PrpD family.Curated

Phylogenomic databases

eggNOGiENOG4105DXD Bacteria
COG2079 LUCA
HOGENOMiHOG000159916
InParanoidiP45859
KOiK01720
OMAiECTKHLG
PhylomeDBiP45859

Family and domain databases

InterProiView protein in InterPro
IPR012705 2Me_IsoCit_deHydtase_PrpD
IPR036148 MmgE/PrpD_sf
IPR005656 MmgE_PrpD
PANTHERiPTHR16943 PTHR16943, 1 hit
PfamiView protein in Pfam
PF03972 MmgE_PrpD, 1 hit
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)DescriptionActionsGraphical viewLength
Sequence conflicti216A → P in BAA12591 (PubMed:8969508).Curated1

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, NZ_JNCM01000036.1

Genome annotation databases

EnsemblBacteriaiCAB14344; CAB14344; BSU24130
GeneIDi938663
KEGGibsu:BSU24130
PATRICifig|224308.43.peg.2517

Similar proteinsi

Entry informationi

Entry nameiPRPD_BACSU
AccessioniPrimary (citable) accession number: P45859
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: July 7, 2009
Last modified: May 23, 2018
This is version 115 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

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