Skip Header

Contribute Send feedback
Read comments (?) or add your own

P38998 (LYS1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 126. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Saccharopine dehydrogenase [NAD(+), L-lysine-forming]

Short name=SDH
EC=1.5.1.7
Alternative name(s):
Lysine--2-oxoglutarate reductase
Gene names
Name:LYS1
Ordered Locus Names:YIR034C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length373 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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

Catalytic activity

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

Enzyme regulation

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. Ref.5 Ref.10 Ref.11

Pathway

Amino-acid biosynthesis; L-lysine biosynthesis via AAA pathway; L-lysine from L-alpha-aminoadipate (fungal route): step 3/3.

Subunit structure

Monomer. Ref.5

Subcellular location

Cytoplasm Ref.13.

Induction

Induced by alpha-aminoadipate semialdehyde in a LYS14-dependent manner. Repressed by lysine. Ref.5 Ref.10 Ref.11 Ref.12

Miscellaneous

Present with 111934 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the AlaDH/PNT family.

Biophysicochemical properties

Kinetic parameters:

KM=0.089 mM for NADH Ref.7 Ref.8

KM=0.1 mM for NAD+

KM=1.67 mM for saccharopine

KM=0.55 mM for 2-oxoglutarate

KM=2.0 mM for L-lysine

pH dependence:

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

Binary interactions

With

Entry

#Exp.

IntAct

Notes

RSP5P399403EBI-10264,EBI-16219

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.4 Ref.5
Chain2 – 373372Saccharopine dehydrogenase [NAD(+), L-lysine-forming]
PRO_0000199016

Sites

Active site2051 Ref.9

Amino acid modifications

Modified residue21N-acetylalanine; partial Ref.4

Experimental info

Sequence conflict2091A → AL AA sequence Ref.6
Sequence conflict3091A → V in CAA54551. Ref.1

Secondary structure

............................................................... 373
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P38998 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 7E3A810876C1DC41

FASTA37341,465
        10         20         30         40         50         60 
MAAVTLHLRA ETKPLEARAA LTPTTVKKLI AKGFKIYVED SPQSTFNINE YRQAGAIIVP 

        70         80         90        100        110        120 
AGSWKTAPRD RIIIGLKEMP ETDTFPLVHE HIQFAHCYKD QAGWQNVLMR FIKGHGTLYD 

       130        140        150        160        170        180 
LEFLENDQGR RVAAFGFYAG FAGAALGVRD WAFKQTHSDD EDLPAVSPYP NEKALVKDVT 

       190        200        210        220        230        240 
KDYKEALATG ARKPTVLIIG ALGRCGSGAI DLLHKVGIPD ANILKWDIKE TSRGGPFDEI 

       250        260        270        280        290        300 
PQADIFINCI YLSKPIAPFT NMEKLNNPNR RLRTVVDVSA DTTNPHNPIP IYTVATVFNK 

       310        320        330        340        350        360 
PTVLVPTTAG PKLSVISIDH LPSLLPREAS EFFSHDLLPS LELLPQRKTA PVWVRAKKLF 

       370 
DRHCARVKRS SRL 

« Hide

References

« Hide 'large scale' references
[1]Feller A.
Submitted (JAN-1994) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: Sigma 1278B.
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome IX."
Churcher C.M., Bowman S., Badcock K., Bankier A.T., Brown D., Chillingworth T., Connor R., Devlin K., Gentles S., Hamlin N., Harris D.E., Horsnell T., Hunt S., Jagels K., Jones M., Lye G., Moule S., Odell C. expand/collapse author list , Pearson D., Rajandream M.A., Rice P., Rowley N., Skelton J., Smith V., Walsh S.V., Whitehead S., Barrell B.G.
Nature 387:84-87(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204511 / S288c / AB972.
[3]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]Bienvenut W.V., Peters C.
Submitted (JUN-2005) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 2-9; 36-65; 132-149; 193-204; 216-225 AND 313-327, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT ALA-2, MASS SPECTROMETRY.
[5]"Purification and characterization of saccharopine dehydrogenase from baker's yeast."
Ogawa H., Fujioka M.
J. Biol. Chem. 253:3666-3670(1978) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-3, CLEAVAGE OF INITIATOR METHIONINE, SUBUNIT, ENZYME REGULATION.
[6]"Amino acid sequence of a peptide containing an essential cysteine residue of yeast saccharopine dehydrogenase (L-lysine-forming)."
Ogawa H., Hase T., Fujioka M.
Biochim. Biophys. Acta 623:225-228(1980) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 203-212.
[7]"Saccharopine, an intermediate of the aminoadipic acid pathway of lysine biosynthesis. IV. Saccharopine dehydrogenase."
Saunders P.P., Broquist H.P.
J. Biol. Chem. 241:3435-3440(1966) [PubMed] [Europe PMC] [Abstract]
Cited for: BIOPHYSICOCHEMICAL PROPERTIES.
[8]"A kinetic study of saccharopine dehydrogenase reaction."
Fujioka M., Nakatani Y.
Eur. J. Biochem. 16:180-186(1970) [PubMed] [Europe PMC] [Abstract]
Cited for: BIOPHYSICOCHEMICAL PROPERTIES.
[9]"Chemical modification of the active site sulfhydryl group of saccharopine dehydrogenase (L-lysine-forming)."
Ogawa H., Okamoto M., Fujioka M.
J. Biol. Chem. 254:7030-7035(1979) [PubMed] [Europe PMC] [Abstract]
Cited for: ACTIVE SITE.
[10]"The inactivation of saccharopine dehydrogenase (L-lysine-forming) by diethyl pyrocarbonate."
Fujioka M., Takata Y., Ogawa H., Okamoto M.
J. Biol. Chem. 255:937-942(1980) [PubMed] [Europe PMC] [Abstract]
Cited for: ENZYME REGULATION.
[11]"The reaction of pyridoxal 5'-phosphate with an essential lysine residue of saccharopine dehydrogenase (L-lysine-forming)."
Ogawa H., Fujioka M.
J. Biol. Chem. 255:7420-7425(1980) [PubMed] [Europe PMC] [Abstract]
Cited for: ENZYME REGULATION.
[12]"Control of enzyme synthesis in the lysine biosynthetic pathway of Saccharomyces cerevisiae. Evidence for a regulatory role of gene LYS14."
Ramos F., Dubois E., Pierard A.
Eur. J. Biochem. 171:171-176(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: INDUCTION.
[13]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[14]"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] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X77362 Genomic DNA. Translation: CAA54551.1.
Z38061 Genomic DNA. Translation: CAA86194.1.
BK006942 Genomic DNA. Translation: DAA08581.1.
PIRS48496.
RefSeqNP_012300.3. NM_001179556.3.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP38998.
SMRP38998. Positions 3-373.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-5291N.
IntActP38998. 10 interactions.
MINTMINT-524089.
STRING4932.YIR034C.

Proteomic databases

PaxDbP38998.
PeptideAtlasP38998.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYIR034C; YIR034C; YIR034C.
GeneID854852.
KEGGsce:YIR034C.

Organism-specific databases

SGDS000001473. LYS1.

Phylogenomic databases

eggNOGNOG79735.
HOGENOMHOG000143704.
KOK00290.
OMAQFAHCYK.
OrthoDBEOG408RHS.

Enzyme and pathway databases

BioCycYEAST:YIR034C-MONOMER.
SABIO-RKP38998.
UniPathwayUPA00033; UER00034.

Gene expression databases

GenevestigatorP38998.
GermOnlineYIR034C. Saccharomyces cerevisiae.

Family and domain databases

InterProIPR007886. AlaDH/PNT_N.
IPR007698. AlaDH/PNT_NAD(H)-bd.
IPR027281. Lys1.
[Graphical view]
PANTHERPTHR11133:SF4. PTHR11133:SF4. 1 hit.
PfamPF01262. AlaDh_PNT_C. 1 hit.
PF05222. AlaDh_PNT_N. 1 hit.
[Graphical view]
PIRSFPIRSF018250. Saccharopine_DH_Lys. 1 hit.
SMARTSM01002. AlaDh_PNT_C. 1 hit.
SM01003. AlaDh_PNT_N. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP38998.
NextBio977755.

Entry information

Entry nameLYS1_YEAST
AccessionPrimary (citable) accession number: P38998
Secondary accession number(s): D6VVW5
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: January 23, 2007
Last modified: May 29, 2013
This is version 126 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast

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

Yeast chromosome IX

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

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