Homoserine dehydrogenase - Saccharomyces cerevisiae (Baker's yeast)

Names and origin

Protein names

Recommended name:
    Homoserine dehydrogenase
      Short name=HDH
    EC=1.1.1.3

Gene names

Name:	HOM6
Ordered Locus Names:	YJR139C
ORF Names:	J2132

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

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Protein attributes

Sequence length	359 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Catalytic activity	L-homoserine + NAD(P)(+) = L-aspartate 4-semialdehyde + NAD(P)H.
Pathway	Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-homoserine from L-aspartate: step 3/3. Amino-acid biosynthesis; L-threonine biosynthesis; L-threonine from L-aspartate: step 3/5.
Subunit structure	Homodimer.
Miscellaneous	Present with 48900 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the homoserine dehydrogenase family.

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Ontologies

Keywords
Biological process	Amino-acid biosynthesis Branched-chain amino acid biosynthesis Isoleucine biosynthesis Methionine biosynthesis Threonine biosynthesis
Ligand	NADP
Molecular function	Oxidoreductase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	methionine metabolic process Traceable author statement. Source: SGD response to drug Inferred from mutant phenotype. Source: SGD threonine metabolic process Traceable author statement. Source: SGD
Cellular component	cytoplasm Inferred from direct assay. Source: SGD nucleus Inferred from direct assay. Source: SGD
Molecular function	homoserine dehydrogenase activity Inferred from direct assay. Source: SGD
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Molecule processing

Chain

1 – 359

359

Homoserine dehydrogenase

Regions

Nucleotide binding

11 – 18

8

NADP

Sites

Active site

223

1

Proton donor Potential

Binding site

93

1

NADP

Binding site

117

1

NADP

Binding site

208

1

Substrate

Amino acid modifications

Modified residue

237

1

Phosphoserine

Modified residue

239

1

Phosphothreonine

Modified residue

344

1

Phosphothreonine

Experimental info

Mutagenesis

117

1

K → A: Loss of activity

Mutagenesis

208

1

E → D: Increases KM for aspartate-semialdehyde 48-fold and reduces Kcat by 50%

Mutagenesis

208

1

E → L or Q: Loss of activity

Mutagenesis

219

1

D → L: Reduces Kcat 150-fold

Mutagenesis

223

1

K → V: Loss of activity

Sequence conflict

134

1

K → L AA sequence Ref.3

Sequence conflict

152

1

Missing AA sequence Ref.3

Sequence conflict

327

1

R → V AA sequence Ref.3

Sequence conflict

333

1

Missing AA sequence Ref.3

Secondary structure

1

.

359

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P31116-1 [UniParc].

Last modified July 1, 1993. Version 1.
Checksum: 6C106F9EB0BD0CC5
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FASTA

359

38,502

        10         20         30         40         50         60 
MSTKVVNVAV IGAGVVGSAF LDQLLAMKST ITYNLVLLAE AERSLISKDF SPLNVGSDWK 

        70         80         90        100        110        120 
AALAASTTKT LPLDDLIAHL KTSPKPVILV DNTSSAYIAG FYTKFVENGI SIATPNKKAF 

       130        140        150        160        170        180 
SSDLATWKAL FSNKPTNGFV YHEATVGAGL PIISFLREII QTGDEVEKIE GIFSGTLSYI 

       190        200        210        220        230        240 
FNEFSTSQAN DVKFSDVVKV AKKLGYTEPD PRDDLNGLDV ARKVTIVGRI SGVEVESPTS 

       250        260        270        280        290        300 
FPVQSLIPKP LESVKSADEF LEKLSDYDKD LTQLKKEAAT ENKVLRFIGK VDVATKSVSV 

       310        320        330        340        350 
GIEKYDYSHP FASLKGSDNV ISIKTKRYTN PVVIQGAGAG AAVTAAGVLG DVIKIAQRL

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Evolutionary relationships between yeast and bacterial homoserine dehydrogenases." Thomas D., Barbey R., Surdin-Kerjan Y. FEBS Lett. 323:289-293(1993) [PubMed: 8500624] [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. Karpfinger-Hartl L. EMBO J. 15:2031-2049(1996) [PubMed: 8641269] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	"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: 1897932] [Abstract] Cited for: PROTEIN SEQUENCE OF 129-158 AND 327-354.
[4]	"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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[5]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-237 AND THR-239, MASS SPECTROMETRY.
[6]	"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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-237 AND THR-344, MASS SPECTROMETRY.
[7]	"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: 10700284] [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.
[8]	"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: 14583265] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG.
[9]	"New phenolic inhibitors of yeast homoserine dehydrogenase." Ejim L., Mirza I.A., Capone C., Nazi I., Jenkins S., Chee G.-L., Berghuis A.M., Wright G.D. Bioorg. Med. Chem. 12:3825-3830(2004) [PubMed: 15210149] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 2-359 IN COMPLEX WITH INHIBITORS.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

X64457 Genomic DNA. Translation: CAA45787.1.
Z49639 Genomic DNA. Translation: CAA89671.1.

PIR

S33317.

RefSeq

NP_012673.1.

3D structure databases

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	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:6315N.

IntAct

P31116.

Proteomic databases

PeptideAtlas

P31116.

Genome annotation databases

Ensembl

YJR139C. Saccharomyces cerevisiae. [Contig view]

GeneID

853604.

GenomeReviews

Gene locus YJR139C in contig Y13136_GR.

KEGG

sce:YJR139C.

NMPDR

fig|4932.3.peg.3649.

Organism-specific databases

CYGD

YJR139c.

SGD

S000003900. HOM6.

Yeast-GFP

Search...

Phylogenomic databases

HOGENOM

P31116.

Gene expression databases

GermOnline

YJR139C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR005106. Asp/hSer_DHase_NAD-bd.
IPR001342. hSer_DHase_cat.
IPR016040. NAD(P)-bd.
[Graphical view]

Gene3D

G3DSA:3.40.50.720. NAD(P)-bd. 1 hit.

Pfam

PF00742. Homoserine_dh. 1 hit.
PF03447. NAD_binding_3. 1 hit.
[Graphical view]

PROSITE

PS01042. HOMOSER_DHGENASE. 1 hit.
[Graphical view]

ProDom

P31116.
[Graphical view] [Entries sharing at least one domain]

BLOCKS

Search...

Other Resources

LinkHub

P31116.

ProtoNet

Search...

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Entry information

Entry name

DHOM_YEAST

Accession

Primary (citable) accession number: P31116

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1993
Last sequence update:	July 1, 1993
Last modified:	September 2, 2008
This is version 73 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)

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Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome X

Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Keywords

Gene Ontology (GO)

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents