Reviewed, UniProtKB/Swiss-Prot P77243 (PRPD_ECOLI)

Names and origin

Protein names

Recommended name:
    2-methylcitrate dehydratase
    EC=4.2.1.79

Gene names

Name:	prpD
Synonyms:	yahT
Ordered Locus Names:	b0334, JW0325

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	483 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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 activity	(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate = (Z)-but-2-ene-1,2,3-tricarboxylate + H2O.
Cofactor	Binds 1 2Fe-2S cluster.
Pathway	Organic acid metabolism; propanoate degradation.
Subunit structure	Monomer.
Sequence similarities	Belongs to the prpD family.

Ontologies

Keywords
Ligand	2Fe-2S Iron Iron-sulfur Metal-binding
Molecular function	Lyase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	propionate catabolic process, 2-methylcitrate cycle Inferred from electronic annotation. Source: InterPro
Molecular function	2 iron, 2 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW 2-methylcitrate dehydratase activity Inferred from electronic annotation. Source: EC iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.4

Chain

2 – 483

482

2-methylcitrate dehydratase

PRO_0000215023

Secondary structure

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483

Helix Strand Turn

Details...

Helix

14 – 25

12

Helix

31 – 51

21

Helix

55 – 58

4

Helix

85 – 98

14

Beta strand

107 – 109

3

Helix

113 – 116

4

Helix

117 – 133

17

Helix

141 – 158

18

Turn

159 – 161

3

Helix

165 – 167

3

Helix

172 – 186

15

Helix

191 – 202

12

Helix

210 – 212

3

Helix

220 – 240

21

Turn

247 – 251

5

Turn

253 – 255

3

Helix

257 – 261

5

Beta strand

273 – 275

3

Helix

276 – 280

5

Beta strand

286 – 288

3

Turn

291 – 293

3

Helix

294 – 309

16

Helix

314 – 316

3

Beta strand

317 – 324

8

Helix

326 – 332

7

Helix

341 – 344

4

Helix

348 – 358

11

Helix

363 – 366

4

Helix

368 – 371

4

Helix

374 – 381

8

Beta strand

383 – 387

5

Helix

389 – 396

8

Turn

398 – 400

3

Beta strand

405 – 411

7

Beta strand

420 – 422

3

Helix

429 – 431

3

Helix

432 – 450

19

Helix

453 – 464

12

Helix

466 – 471

6

Helix

474 – 478

5

Turn

479 – 481

3

Sequences

	Sequence		Length	Mass (Da)
	P77243-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 965252C8983E6F64	FASTA	483	53,952
	10 20 30 40 50 60 MSAQINNIRP EFDREIVDIV DYVMNYEISS KVAYDTAHYC LLDTLGCGLE ALEYPACKKL 70 80 90 100 110 120 LGPIVPGTVV PNGVRVPGTQ FQLDPVQAAF NIGAMIRWLD FNDTWLAAEW GHPSDNLGGI 130 140 150 160 170 180 LATADWLSRN AVASGKAPLT MKQVLTAMIK AHEIQGCIAL ENSFNRVGLD HVLLVKVAST 190 200 210 220 230 240 AVVAEMLGLT REEILNAVSL AWVDGQSLRT YRHAPNTGTR KSWAAGDATS RAVRLALMAK 250 260 270 280 290 300 TGEMGYPSAL TAPVWGFYDV SFKGESFRFQ RPYGSYVMEN VLFKISFPAE FHSQTAVEAA 310 320 330 340 350 360 MTLYEQMQAA GKTAADIEKV TIRTHEACIR IIDKKGPLNN PADRDHCIQY MVAIPLLFGR 370 380 390 400 410 420 LTAADYEDNV AQDKRIDALR EKINCFEDPA FTADYHDPEK RAIANAITLE FTDGTRFEEV 430 440 450 460 470 480 VVEYPIGHAR RRQDGIPKLV DKFKINLARQ FPTRQQQRIL EVSLDRARLE QMPVNEYLDL YVI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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 (JAN-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[2]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] 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(2006) [PubMed: 16738553] [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(2002) [PubMed: 11782506] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-13, CHARACTERIZATION.

Cross-references

Sequence databases

EMBLGenBankDDBJ

U73857 Genomic DNA. Translation: AAB18058.1.
U00096 Genomic DNA. Translation: AAC73437.1.
AP009048 Genomic DNA. Translation: BAE76116.1.

PIR

F64760.

RefSeq

AP_000986.1.
NP_414868.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1SZQ	X-ray	2.70	A/B	1-483	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:10580N.

STRING

P77243.

Genome annotation databases

GeneID

945931.

GenomeReviews

Gene locus JW0325 in contig AP009048_GR.
Gene locus b0334 in contig U00096_GR.

KEGG

ecj:JW0325.
eco:b0334.

Organism-specific databases

EchoBASE

EB3371.

EcoGene

EG13603. prpD.

CMR

Search...

Phylogenomic databases

HOGENOM

P77243.

OMA

ALRFPEC.

Enzyme and pathway databases

BioCyc

EcoCyc:G6199-MON.
MetaCyc:G6199-MON.

BRENDA

4.2.1.79. 246.

Gene expression databases

Genevestigator

P77243.

Family and domain databases

InterPro

IPR012705. 2Me_IsoCit_deHydtase_PrpD.
IPR005656. MmgE_PrpD.
[Graphical view]

PANTHER

PTHR16943. MmgE_PrpD. 1 hit.

Pfam

PF03972. MmgE_PrpD. 1 hit.
[Graphical view]

TIGRFAMs

TIGR02330. prpD. 1 hit.

ProtoNet

Search...

Entry information

Entry name

PRPD_ECOLI

Accession

Primary (citable) accession number: P77243
Secondary accession number(s): Q2MC90

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	January 23, 2007
Last modified:	November 3, 2009
This is version 81 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)