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P31116

- DHOM_YEAST

UniProt

P31116 - DHOM_YEAST

Protein

Homoserine dehydrogenase

Gene

HOM6

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 124 (01 Oct 2014)
      Sequence version 1 (01 Jul 1993)
      Previous versions | rss
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    Functioni

    Catalytic activityi

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

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei93 – 931NADP1 Publication
    Binding sitei117 – 1171NADP1 Publication
    Binding sitei208 – 2081Substrate1 Publication
    Active sitei223 – 2231Proton donorSequence Analysis

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi11 – 188NADP1 Publication

    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

    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.3 Publications

    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP31116.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the homoserine dehydrogenase family.Curated

    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

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti134 – 1341K → L AA sequence (PubMed:1897932)Curated
    Sequence conflicti152 – 1521Missing AA sequence (PubMed:1897932)Curated
    Sequence conflicti327 – 3271R → V AA sequence (PubMed:1897932)Curated
    Sequence conflicti333 – 3331Missing AA sequence (PubMed:1897932)Curated

    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

    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: October 1, 2014
    This is version 124 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

    External Data

    Dasty 3