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Protein

Homoserine dehydrogenase

Gene

HOM6

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: 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: L-methionine biosynthesis via de novo pathway

This protein is involved in step 3 of the subpathway that synthesizes L-homoserine from L-aspartate.
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. Aspartokinase (HOM3)
  2. Aspartate-semialdehyde dehydrogenase (HOM2)
  3. Homoserine dehydrogenase (HOM6)
This subpathway is part of the pathway L-methionine biosynthesis via de novo pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-homoserine from L-aspartate, the pathway L-methionine biosynthesis via de novo pathway and in Amino-acid biosynthesis.

Pathwayi: L-threonine biosynthesis

This protein is involved in step 3 of the subpathway that synthesizes L-threonine from L-aspartate.
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. Aspartokinase (HOM3)
  2. Aspartate-semialdehyde dehydrogenase (HOM2)
  3. Homoserine dehydrogenase (HOM6)
  4. Homoserine kinase (THR1)
  5. Threonine synthase (THR4)
This subpathway is part of the pathway L-threonine biosynthesis, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-threonine from L-aspartate, the pathway L-threonine biosynthesis and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei93NADP1 Publication1
Binding sitei117NADP1 Publication1
Binding sitei208Substrate1 Publication1
Active sitei223Proton donorSequence analysis1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi11 – 18NADP1 Publication8

GO - Molecular functioni

  • aspartate kinase activity Source: GO_Central
  • homoserine dehydrogenase activity Source: SGD
  • NADP binding Source: InterPro

GO - Biological processi

  • homoserine biosynthetic process Source: SGD
  • isoleucine biosynthetic process Source: UniProtKB-KW
  • lysine biosynthetic process via diaminopimelate Source: GO_Central
  • methionine biosynthetic process Source: SGD
  • 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.
BRENDAi1.1.1.3. 984.
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
Proteomesi
  • UP000002311 Componenti: Chromosome X

Organism-specific databases

EuPathDBiFungiDB:YJR139C.
SGDiS000003900. HOM6.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi117K → A: Loss of activity. 1
Mutagenesisi208E → D: Increases KM for aspartate-semialdehyde 48-fold and reduces Kcat by 50%. 1 Publication1
Mutagenesisi208E → L or Q: Loss of activity. 1 Publication1
Mutagenesisi219D → L: Reduces Kcat 150-fold. 1 Publication1
Mutagenesisi223K → V: Loss of activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000667071 – 359Homoserine dehydrogenaseAdd BLAST359

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki290Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

MaxQBiP31116.
PRIDEiP31116.
TopDownProteomicsiP31116.

PTM databases

iPTMnetiP31116.

Interactioni

Subunit structurei

Homodimer.3 Publications

Protein-protein interaction databases

BioGridi33895. 273 interactors.
DIPiDIP-6315N.
IntActiP31116. 6 interactors.
MINTiMINT-2731902.

Structurei

Secondary structure

1359
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 11Combined sources8
Helixi15 – 26Combined sources12
Beta strandi30 – 39Combined sources10
Beta strandi41 – 46Combined sources6
Turni54 – 57Combined sources4
Helixi59 – 64Combined sources6
Helixi73 – 80Combined sources8
Beta strandi87 – 91Combined sources5
Helixi96 – 99Combined sources4
Helixi102 – 107Combined sources6
Beta strandi111 – 113Combined sources3
Helixi118 – 120Combined sources3
Helixi124 – 130Combined sources7
Beta strandi135 – 137Combined sources3
Helixi143 – 145Combined sources3
Turni146 – 149Combined sources4
Beta strandi150 – 152Combined sources3
Helixi153 – 162Combined sources10
Beta strandi166 – 172Combined sources7
Helixi175 – 184Combined sources10
Helixi194 – 204Combined sources11
Helixi212 – 215Combined sources4
Helixi218 – 230Combined sources13
Helixi249 – 251Combined sources3
Beta strandi255 – 257Combined sources3
Helixi258 – 264Combined sources7
Helixi265 – 267Combined sources3
Helixi268 – 278Combined sources11
Turni279 – 282Combined sources4
Beta strandi283 – 292Combined sources10
Turni293 – 296Combined sources4
Beta strandi297 – 309Combined sources13
Helixi310 – 313Combined sources4
Beta strandi319 – 327Combined sources9
Beta strandi332 – 336Combined sources5
Helixi341 – 358Combined sources18

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP31116.

Family & Domainsi

Sequence similaritiesi

Belongs to the homoserine dehydrogenase family.Curated

Phylogenomic databases

HOGENOMiHOG000024037.
InParanoidiP31116.
KOiK00003.
OMAiVYHEATV.
OrthoDBiEOG092C36D3.

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.
SUPFAMiSSF51735. SSF51735. 1 hit.
PROSITEiPS01042. HOMOSER_DHGENASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P31116-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTKVVNVAV IGAGVVGSAF LDQLLAMKST ITYNLVLLAE AERSLISKDF
60 70 80 90 100
SPLNVGSDWK AALAASTTKT LPLDDLIAHL KTSPKPVILV DNTSSAYIAG
110 120 130 140 150
FYTKFVENGI SIATPNKKAF SSDLATWKAL FSNKPTNGFV YHEATVGAGL
160 170 180 190 200
PIISFLREII QTGDEVEKIE GIFSGTLSYI FNEFSTSQAN DVKFSDVVKV
210 220 230 240 250
AKKLGYTEPD PRDDLNGLDV ARKVTIVGRI SGVEVESPTS FPVQSLIPKP
260 270 280 290 300
LESVKSADEF LEKLSDYDKD LTQLKKEAAT ENKVLRFIGK VDVATKSVSV
310 320 330 340 350
GIEKYDYSHP FASLKGSDNV ISIKTKRYTN PVVIQGAGAG AAVTAAGVLG

DVIKIAQRL
Length:359
Mass (Da):38,502
Last modified:July 1, 1993 - v1
Checksum:i6C106F9EB0BD0CC5
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti134K → L AA sequence (PubMed:1897932).Curated1
Sequence conflicti152Missing AA sequence (PubMed:1897932).Curated1
Sequence conflicti327R → V AA sequence (PubMed:1897932).Curated1
Sequence conflicti333Missing AA sequence (PubMed:1897932).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33895. 273 interactors.
DIPiDIP-6315N.
IntActiP31116. 6 interactors.
MINTiMINT-2731902.

PTM databases

iPTMnetiP31116.

Proteomic databases

MaxQBiP31116.
PRIDEiP31116.
TopDownProteomicsiP31116.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YJR139C.
SGDiS000003900. HOM6.

Phylogenomic databases

HOGENOMiHOG000024037.
InParanoidiP31116.
KOiK00003.
OMAiVYHEATV.
OrthoDBiEOG092C36D3.

Enzyme and pathway databases

UniPathwayiUPA00050; UER00063.
UPA00051; UER00465.
BioCyciYEAST:YJR139C-MONOMER.
BRENDAi1.1.1.3. 984.

Miscellaneous databases

EvolutionaryTraceiP31116.
PROiP31116.

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.
SUPFAMiSSF51735. SSF51735. 1 hit.
PROSITEiPS01042. HOMOSER_DHGENASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

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: November 2, 2016
This is version 144 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.1 Publication

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.