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Protein

Saccharopine dehydrogenase [NAD(+), L-lysine-forming]

Gene

LYS1

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

Catalyzes the NAD+-dependent cleavage of saccharopine to L-lysine and 2-oxoglutarate.

Catalytic activityi

N(6)-(L-1,3-dicarboxypropyl)-L-lysine + NAD+ + H2O = L-lysine + 2-oxoglutarate + NADH.

Enzyme regulationi

Inhibited by p-chloromercuribenzoate and iodoacetate by modification of the active site cysteine residue. Inhibited by diethyl pyrocarbonate by modification of histidine residues. Inhibited by pyridoxal 5'-phosphate by modification of an essential lysine residue.3 Publications

Kineticsi

  1. KM=0.089 mM for NADH2 Publications
  2. KM=0.1 mM for NAD+2 Publications
  3. KM=1.67 mM for saccharopine2 Publications
  4. KM=0.55 mM for 2-oxoglutarate2 Publications
  5. KM=2.0 mM for L-lysine2 Publications

    pH dependencei

    Optimum pH is 10 for the forward reaction, and 6.5-7 for the reverse reaction.2 Publications

    Pathwayi: L-lysine biosynthesis via AAA pathway

    This protein is involved in step 3 of the subpathway that synthesizes L-lysine from L-alpha-aminoadipate (fungal route).
    Proteins known to be involved in the 3 steps of the subpathway in this organism are:
    1. L-2-aminoadipate reductase (LYS2)
    2. Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] (LYS9)
    3. Saccharopine dehydrogenase [NAD(+), L-lysine-forming] (LYS1)
    This subpathway is part of the pathway L-lysine biosynthesis via AAA 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-lysine from L-alpha-aminoadipate (fungal route), the pathway L-lysine biosynthesis via AAA pathway and in Amino-acid biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei205 – 20511 Publication

    GO - Molecular functioni

    • mRNA binding Source: SGD
    • saccharopine dehydrogenase (NAD+, L-lysine-forming) activity Source: SGD

    GO - Biological processi

    • lysine biosynthetic process Source: SGD
    • lysine biosynthetic process via aminoadipic acid Source: SGD
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Amino-acid biosynthesis, Lysine biosynthesis

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciYEAST:YIR034C-MONOMER.
    BRENDAi1.5.1.7. 984.
    SABIO-RKP38998.
    UniPathwayiUPA00033; UER00034.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Saccharopine dehydrogenase [NAD(+), L-lysine-forming] (EC:1.5.1.7)
    Short name:
    SDH
    Alternative name(s):
    Lysine--2-oxoglutarate reductase
    Gene namesi
    Name:LYS1
    Ordered Locus Names:YIR034C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome IX

    Organism-specific databases

    EuPathDBiFungiDB:YIR034C.
    SGDiS000001473. LYS1.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved2 Publications
    Chaini2 – 373372Saccharopine dehydrogenase [NAD(+), L-lysine-forming]PRO_0000199016Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylalanine; partial1 Publication

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiP38998.

    Expressioni

    Inductioni

    Induced by alpha-aminoadipate semialdehyde in a LYS14-dependent manner. Repressed by lysine.1 Publication

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    RSP5P399403EBI-10264,EBI-16219

    Protein-protein interaction databases

    BioGridi35025. 19 interactions.
    DIPiDIP-5291N.
    IntActiP38998. 7 interactions.
    MINTiMINT-524089.

    Structurei

    Secondary structure

    1
    373
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 84Combined sources
    Helixi23 – 319Combined sources
    Beta strandi35 – 395Combined sources
    Beta strandi44 – 463Combined sources
    Helixi48 – 536Combined sources
    Beta strandi57 – 593Combined sources
    Helixi63 – 664Combined sources
    Beta strandi71 – 744Combined sources
    Beta strandi89 – 935Combined sources
    Helixi104 – 11411Combined sources
    Beta strandi117 – 1204Combined sources
    Helixi121 – 1233Combined sources
    Beta strandi131 – 1333Combined sources
    Helixi136 – 15621Combined sources
    Helixi172 – 18716Combined sources
    Turni188 – 1903Combined sources
    Beta strandi196 – 2005Combined sources
    Helixi204 – 21512Combined sources
    Helixi220 – 2223Combined sources
    Beta strandi223 – 2264Combined sources
    Helixi228 – 2314Combined sources
    Helixi239 – 2424Combined sources
    Beta strandi243 – 2486Combined sources
    Helixi262 – 2654Combined sources
    Beta strandi274 – 2774Combined sources
    Beta strandi303 – 3053Combined sources
    Beta strandi308 – 3114Combined sources
    Beta strandi313 – 3164Combined sources
    Helixi321 – 3244Combined sources
    Helixi326 – 34217Combined sources
    Turni345 – 3495Combined sources
    Helixi351 – 36515Combined sources
    Helixi370 – 3723Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2Q99X-ray1.64A1-373[»]
    2QRJX-ray1.60A1-373[»]
    2QRKX-ray1.75A1-373[»]
    2QRLX-ray1.60A1-373[»]
    3UGKX-ray2.01A1-373[»]
    3UH1X-ray2.17A1-373[»]
    3UHAX-ray2.30A/B1-373[»]
    ProteinModelPortaliP38998.
    SMRiP38998. Positions 3-373.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP38998.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the AlaDH/PNT family.Curated

    Phylogenomic databases

    HOGENOMiHOG000143704.
    InParanoidiP38998.
    KOiK00290.
    OMAiFGYWAGY.
    OrthoDBiEOG092C2ZET.

    Family and domain databases

    InterProiIPR007886. AlaDH/PNT_N.
    IPR007698. AlaDH/PNT_NAD(H)-bd.
    IPR027281. Lys1.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF05222. AlaDh_PNT_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF018250. Saccharopine_DH_Lys. 1 hit.
    SMARTiSM01002. AlaDh_PNT_C. 1 hit.
    SM01003. AlaDh_PNT_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF51735. SSF51735. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P38998-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAAVTLHLRA ETKPLEARAA LTPTTVKKLI AKGFKIYVED SPQSTFNINE
    60 70 80 90 100
    YRQAGAIIVP AGSWKTAPRD RIIIGLKEMP ETDTFPLVHE HIQFAHCYKD
    110 120 130 140 150
    QAGWQNVLMR FIKGHGTLYD LEFLENDQGR RVAAFGFYAG FAGAALGVRD
    160 170 180 190 200
    WAFKQTHSDD EDLPAVSPYP NEKALVKDVT KDYKEALATG ARKPTVLIIG
    210 220 230 240 250
    ALGRCGSGAI DLLHKVGIPD ANILKWDIKE TSRGGPFDEI PQADIFINCI
    260 270 280 290 300
    YLSKPIAPFT NMEKLNNPNR RLRTVVDVSA DTTNPHNPIP IYTVATVFNK
    310 320 330 340 350
    PTVLVPTTAG PKLSVISIDH LPSLLPREAS EFFSHDLLPS LELLPQRKTA
    360 370
    PVWVRAKKLF DRHCARVKRS SRL
    Length:373
    Mass (Da):41,465
    Last modified:January 23, 2007 - v3
    Checksum:i7E3A810876C1DC41
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti209 – 2091A → AL AA sequence (PubMed:6769500).Curated
    Sequence conflicti309 – 3091A → V in CAA54551 (Ref. 1) Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X77362 Genomic DNA. Translation: CAA54551.1.
    Z38061 Genomic DNA. Translation: CAA86194.1.
    BK006942 Genomic DNA. Translation: DAA08581.1.
    PIRiS48496.
    RefSeqiNP_012300.3. NM_001179556.3.

    Genome annotation databases

    EnsemblFungiiYIR034C; YIR034C; YIR034C.
    GeneIDi854852.
    KEGGisce:YIR034C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X77362 Genomic DNA. Translation: CAA54551.1.
    Z38061 Genomic DNA. Translation: CAA86194.1.
    BK006942 Genomic DNA. Translation: DAA08581.1.
    PIRiS48496.
    RefSeqiNP_012300.3. NM_001179556.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2Q99X-ray1.64A1-373[»]
    2QRJX-ray1.60A1-373[»]
    2QRKX-ray1.75A1-373[»]
    2QRLX-ray1.60A1-373[»]
    3UGKX-ray2.01A1-373[»]
    3UH1X-ray2.17A1-373[»]
    3UHAX-ray2.30A/B1-373[»]
    ProteinModelPortaliP38998.
    SMRiP38998. Positions 3-373.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi35025. 19 interactions.
    DIPiDIP-5291N.
    IntActiP38998. 7 interactions.
    MINTiMINT-524089.

    Proteomic databases

    MaxQBiP38998.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYIR034C; YIR034C; YIR034C.
    GeneIDi854852.
    KEGGisce:YIR034C.

    Organism-specific databases

    EuPathDBiFungiDB:YIR034C.
    SGDiS000001473. LYS1.

    Phylogenomic databases

    HOGENOMiHOG000143704.
    InParanoidiP38998.
    KOiK00290.
    OMAiFGYWAGY.
    OrthoDBiEOG092C2ZET.

    Enzyme and pathway databases

    UniPathwayiUPA00033; UER00034.
    BioCyciYEAST:YIR034C-MONOMER.
    BRENDAi1.5.1.7. 984.
    SABIO-RKP38998.

    Miscellaneous databases

    EvolutionaryTraceiP38998.
    PROiP38998.

    Family and domain databases

    InterProiIPR007886. AlaDH/PNT_N.
    IPR007698. AlaDH/PNT_NAD(H)-bd.
    IPR027281. Lys1.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF05222. AlaDh_PNT_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF018250. Saccharopine_DH_Lys. 1 hit.
    SMARTiSM01002. AlaDh_PNT_C. 1 hit.
    SM01003. AlaDh_PNT_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF51735. SSF51735. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiLYS1_YEAST
    AccessioniPrimary (citable) accession number: P38998
    Secondary accession number(s): D6VVW5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: January 23, 2007
    Last modified: September 7, 2016
    This is version 150 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 111934 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 IX
      Yeast (Saccharomyces cerevisiae) chromosome IX: 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.