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P31116

- DHOM_YEAST

UniProt

P31116 - DHOM_YEAST

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Protein

Homoserine dehydrogenase

Gene
HOM6, YJR139C, J2132
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalytic activityi

L-homoserine + NAD(P)+ = L-aspartate 4-semialdehyde + NAD(P)H.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei93 – 931NADP
Binding sitei117 – 1171NADP
Binding sitei208 – 2081Substrate
Active sitei223 – 2231Proton donor Reviewed prediction

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi11 – 188NADP

GO - Molecular functioni

  1. homoserine dehydrogenase activity Source: SGD
  2. NADP binding Source: InterPro

GO - Biological processi

  1. homoserine biosynthetic process Source: SGD
  2. isoleucine biosynthetic process Source: UniProtKB-KW
  3. methionine biosynthetic process Source: SGD
  4. threonine biosynthetic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Amino-acid biosynthesis, Branched-chain amino acid biosynthesis, Isoleucine biosynthesis, Methionine biosynthesis, Threonine biosynthesis

Keywords - Ligandi

NADP

Enzyme and pathway databases

BioCyciYEAST:YJR139C-MONOMER.
UniPathwayiUPA00050; UER00063.
UPA00051; UER00465.

Names & Taxonomyi

Protein namesi
Recommended name:
Homoserine dehydrogenase (EC:1.1.1.3)
Short name:
HDH
Gene namesi
Name:HOM6
Ordered Locus Names:YJR139C
ORF Names:J2132
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome X

Organism-specific databases

CYGDiYJR139c.
SGDiS000003900. HOM6.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi117 – 1171K → A: Loss of activity.
Mutagenesisi208 – 2081E → D: Increases KM for aspartate-semialdehyde 48-fold and reduces Kcat by 50%. 1 Publication
Mutagenesisi208 – 2081E → L or Q: Loss of activity. 1 Publication
Mutagenesisi219 – 2191D → L: Reduces Kcat 150-fold. 1 Publication
Mutagenesisi223 – 2231K → V: Loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 359359Homoserine dehydrogenasePRO_0000066707Add
BLAST

Proteomic databases

MaxQBiP31116.
PaxDbiP31116.
PeptideAtlasiP31116.

Expressioni

Gene expression databases

GenevestigatoriP31116.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

BioGridi33895. 269 interactions.
DIPiDIP-6315N.
IntActiP31116. 6 interactions.
MINTiMINT-2731902.

Structurei

Secondary structure

1
359
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 118
Helixi15 – 2612
Beta strandi30 – 3910
Beta strandi41 – 466
Turni54 – 574
Helixi59 – 646
Helixi73 – 808
Beta strandi87 – 915
Helixi96 – 994
Helixi102 – 1076
Beta strandi111 – 1133
Helixi118 – 1203
Helixi124 – 1307
Beta strandi135 – 1373
Helixi143 – 1453
Turni146 – 1494
Beta strandi150 – 1523
Helixi153 – 16210
Beta strandi166 – 1727
Helixi175 – 18410
Helixi194 – 20411
Helixi212 – 2154
Helixi218 – 23013
Helixi249 – 2513
Beta strandi255 – 2573
Helixi258 – 2647
Helixi265 – 2673
Helixi268 – 27811
Turni279 – 2824
Beta strandi283 – 29210
Turni293 – 2964
Beta strandi297 – 30913
Helixi310 – 3134
Beta strandi319 – 3279
Beta strandi332 – 3365
Helixi341 – 35818

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EBFX-ray2.30A/B2-359[»]
1EBUX-ray2.60A/B/C/D2-359[»]
1Q7GX-ray2.60A/B1-359[»]
1TVEX-ray3.00A/B2-359[»]
ProteinModelPortaliP31116.
SMRiP31116. Positions 2-359.

Miscellaneous databases

EvolutionaryTraceiP31116.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0460.
HOGENOMiHOG000024037.
KOiK00003.
OMAiYTEPHPA.
OrthoDBiEOG7BGHWP.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
InterProiIPR005106. Asp/hSer_DH_NAD-bd.
IPR001342. HDH_cat.
IPR019811. HDH_CS.
IPR022697. HDH_short.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF00742. Homoserine_dh. 1 hit.
PF03447. NAD_binding_3. 1 hit.
[Graphical view]
PIRSFiPIRSF036497. HDH_short. 1 hit.
PROSITEiPS01042. HOMOSER_DHGENASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P31116-1 [UniParc]FASTAAdd to Basket

« Hide

MSTKVVNVAV IGAGVVGSAF LDQLLAMKST ITYNLVLLAE AERSLISKDF    50
SPLNVGSDWK AALAASTTKT LPLDDLIAHL KTSPKPVILV DNTSSAYIAG 100
FYTKFVENGI SIATPNKKAF SSDLATWKAL FSNKPTNGFV YHEATVGAGL 150
PIISFLREII QTGDEVEKIE GIFSGTLSYI FNEFSTSQAN DVKFSDVVKV 200
AKKLGYTEPD PRDDLNGLDV ARKVTIVGRI SGVEVESPTS FPVQSLIPKP 250
LESVKSADEF LEKLSDYDKD LTQLKKEAAT ENKVLRFIGK VDVATKSVSV 300
GIEKYDYSHP FASLKGSDNV ISIKTKRYTN PVVIQGAGAG AAVTAAGVLG 350
DVIKIAQRL 359
Length:359
Mass (Da):38,502
Last modified:July 1, 1993 - v1
Checksum:i6C106F9EB0BD0CC5
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti134 – 1341K → L AA sequence 1 Publication
Sequence conflicti152 – 1521Missing AA sequence 1 Publication
Sequence conflicti327 – 3271R → V AA sequence 1 Publication
Sequence conflicti333 – 3331Missing AA sequence 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X64457 Genomic DNA. Translation: CAA45787.1.
Z49639 Genomic DNA. Translation: CAA89671.1.
BK006943 Genomic DNA. Translation: DAA08924.1.
PIRiS33317.
RefSeqiNP_012673.3. NM_001181797.3.

Genome annotation databases

EnsemblFungiiYJR139C; YJR139C; YJR139C.
GeneIDi853604.
KEGGisce:YJR139C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X64457 Genomic DNA. Translation: CAA45787.1 .
Z49639 Genomic DNA. Translation: CAA89671.1 .
BK006943 Genomic DNA. Translation: DAA08924.1 .
PIRi S33317.
RefSeqi NP_012673.3. NM_001181797.3.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1EBF X-ray 2.30 A/B 2-359 [» ]
1EBU X-ray 2.60 A/B/C/D 2-359 [» ]
1Q7G X-ray 2.60 A/B 1-359 [» ]
1TVE X-ray 3.00 A/B 2-359 [» ]
ProteinModelPortali P31116.
SMRi P31116. Positions 2-359.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 33895. 269 interactions.
DIPi DIP-6315N.
IntActi P31116. 6 interactions.
MINTi MINT-2731902.

Proteomic databases

MaxQBi P31116.
PaxDbi P31116.
PeptideAtlasi P31116.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YJR139C ; YJR139C ; YJR139C .
GeneIDi 853604.
KEGGi sce:YJR139C.

Organism-specific databases

CYGDi YJR139c.
SGDi S000003900. HOM6.

Phylogenomic databases

eggNOGi COG0460.
HOGENOMi HOG000024037.
KOi K00003.
OMAi YTEPHPA.
OrthoDBi EOG7BGHWP.

Enzyme and pathway databases

UniPathwayi UPA00050 ; UER00063 .
UPA00051 ; UER00465 .
BioCyci YEAST:YJR139C-MONOMER.

Miscellaneous databases

EvolutionaryTracei P31116.
NextBioi 974436.

Gene expression databases

Genevestigatori P31116.

Family and domain databases

Gene3Di 3.40.50.720. 1 hit.
InterProi IPR005106. Asp/hSer_DH_NAD-bd.
IPR001342. HDH_cat.
IPR019811. HDH_CS.
IPR022697. HDH_short.
IPR016040. NAD(P)-bd_dom.
[Graphical view ]
Pfami PF00742. Homoserine_dh. 1 hit.
PF03447. NAD_binding_3. 1 hit.
[Graphical view ]
PIRSFi PIRSF036497. HDH_short. 1 hit.
PROSITEi PS01042. HOMOSER_DHGENASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Evolutionary relationships between yeast and bacterial homoserine dehydrogenases."
    Thomas D., Barbey R., Surdin-Kerjan Y.
    FEBS Lett. 323:289-293(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 26786 / X2180-1A.
  2. "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."
    Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K.
    , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
    EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "Rapid purification and characterization of homoserine dehydrogenase from Saccharomyces cerevisiae."
    Yumoto N., Kawata Y., Noda S., Tokushige M.
    Arch. Biochem. Biophys. 285:270-275(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 129-158 AND 327-354.
  5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  6. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  7. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "Sites of ubiquitin attachment in Saccharomyces cerevisiae."
    Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
    Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "Crystal structures of homoserine dehydrogenase suggest a novel catalytic mechanism for oxidoreductases."
    DeLaBarre B., Thompson P.R., Wright G.D., Berghuis A.M.
    Nat. Struct. Biol. 7:238-244(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 2-359 IN COMPLEX WITH NAD AND SUBSTRATE, MUTAGENESIS OF GLU-208; ASP-219 AND LYS-223.
  10. "Enzyme-assisted suicide: molecular basis for the antifungal activity of 5-hydroxy-4-oxonorvaline by potent inhibition of homoserine dehydrogenase."
    Jacques S.L., Mirza I.A., Ejim L., Koteva K., Hughes D.W., Green K., Kinach R., Honek J.F., Lai H.K., Berghuis A.M., Wright G.D.
    Chem. Biol. 10:989-995(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG.
  11. Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 2-359 IN COMPLEX WITH INHIBITORS.

Entry informationi

Entry nameiDHOM_YEAST
AccessioniPrimary (citable) accession number: P31116
Secondary accession number(s): D6VWV8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 1, 1993
Last modified: May 14, 2014
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 48900 molecules/cell in log phase SD medium.

Keywords - Technical termi

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

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome X
    Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

External Data

Dasty 3

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