Q12428 (PRPD_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Probable 2-methylcitrate dehydratase
EC=4.2.1.79

Gene names

Name:	PDH1
Ordered Locus Names:	YPR002W
ORF Names:	LPZ2W, YP9723.02

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	516 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the dehydration of 2-methylcitrate to 2-methyl-cis-aconitate By similarity.
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 By similarity.
Pathway	Organic acid metabolism; propanoate degradation.
Miscellaneous	Present with 2730 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the PrpD family.

Ontologies

Keywords
Ligand	2Fe-2S Iron Iron-sulfur Metal-binding
Molecular function	Lyase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	propionate catabolic process, 2-methylcitrate cycle Inferred from sequence alignment PubMed 9006051. Source: SGD
Cellular_component	mitochondrial outer membrane Inferred from direct assay PubMed 16407407. Source: SGD
Molecular_function	2 iron, 2 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW 2-methylcitrate dehydratase activity Inferred from sequence alignment PubMed 9006051. Source: SGD metal 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
	Chain	1 – 516	516	Probable 2-methylcitrate dehydratase		PRO_0000215027

Sequences

	Sequence		Length	Mass (Da)
	Q12428 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 2ED7F1AF648F2AAC	FASTA	516	57,684
	10 20 30 40 50 60 MFLAKNLKNN KIKVCLPKKK FAALSTASIQ TNERPNPDKV LKDIAKYVHE TPLKSSLALD 70 80 90 100 110 120 TARLCFLDTL GCGLAALKFK QAQNIIKPIV PGTIVPSGTK ILGTSYVMDP VKGAFAIGTL 130 140 150 160 170 180 IRWLDYNDCW LAAEWGHPSD NLGGILAVAD HLSRLNKATH GKNGKQFLVK DVLEAMIKAH 190 200 210 220 230 240 EIQGIIALEN SFNKVGLDHV VLVKVATAGV VSKMLGLSQE QTIEALSQAF VDGQSLRTYR 250 260 270 280 290 300 HAPNTGSRKS WAAGDAVSRA VNLAYLVKNA NVGTIPSVLT ARTWGFYDVL FKGKPFSFQQ 310 320 330 340 350 360 RSKYDSYVME NVLFKISFPA EFHAQTAVEA AVKAYRILAK QGKTFKDIKS IRIRTQEAAM 370 380 390 400 410 420 RIIDKSGPLY NYADRDHCIQ YMIAVPLITG NLTATDYSDE VARNPEIDNL RSKMYCIEDT 430 440 450 460 470 480 HLTQNYHDPD KRSIGNALLI ELNDGTQLDE IFVEYPVGHK FRREEGIPLL MNKFQRHLRE 490 500 510 HFVESPDKVD LIMKVSSKTN FLNMQIDKYM DLFTEG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI." Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M. , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J. Nature 387:103-105(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	Z71255 Genomic DNA. Translation: CAA95042.1. Z48951 Genomic DNA. Translation: CAA88780.1. U31900 Genomic DNA. Translation: AAA97581.1. BK006949 Genomic DNA. Translation: DAA11429.1.
PIR	S52815.
RefSeq	NP_015326.1. NM_001184099.1.
3D structure databases
ProteinModelPortal	Q12428.
SMR	Q12428. Positions 38-513.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q12428. 1 interaction.
MINT	MINT-2784533.
STRING	4932.YPR002W.
Proteomic databases
PaxDb	Q12428.
PeptideAtlas	Q12428.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YPR002W; YPR002W; YPR002W.
GeneID	856108.
KEGG	sce:YPR002W.
Organism-specific databases
CYGD	YPR002w.
SGD	S000006206. PDH1.
Phylogenomic databases
eggNOG	COG2079.
HOGENOM	HOG000159916.
KO	K01720.
OMA	PNAGSRK.
OrthoDB	EOG44XNR9.
Enzyme and pathway databases
UniPathway	UPA00946.
Gene expression databases
Genevestigator	Q12428.
GermOnline	YPR002W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR012705. 2Me_IsoCit_deHydtase_PrpD. IPR005656. MmgE_PrpD. [Graphical view]
PANTHER	PTHR16943. PTHR16943. 1 hit.
Pfam	PF03972. MmgE_PrpD. 1 hit. [Graphical view]
SUPFAM	SSF103378. MmgE_PrpD. 1 hit.
TIGRFAMs	TIGR02330. prpD. 1 hit.
ProtoNet	Search...
Other
NextBio	981170.

Entry information

Entry name

PRPD_YEAST

Accession

Primary (citable) accession number: Q12428
Secondary accession number(s): D6W413

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1996
Last modified:	May 1, 2013
This is version 100 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program