Saccharopine dehydrogenase [NAD(+), L-lysine-forming] - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P38998 (LYS1_YEAST) Reviewed, UniProtKB/Swiss-Prot

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

Clusters with 100%, 90%, 50% identity |

Documents (5) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended 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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	373 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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: K_M=0.089 mM for NADH Ref.7 Ref.8 K_M=0.1 mM for NAD⁺ K_M=1.67 mM for saccharopine K_M=0.55 mM for 2-oxoglutarate K_M=2.0 mM for L-lysine pH dependence: Optimum pH is 10 for the forward reaction, and 6.5-7 for the reverse reaction.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Lysine biosynthesis
Cellular component	Cytoplasm
Ligand	NAD
Molecular function	Oxidoreductase
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	lysine biosynthetic process via aminoadipic acid Non-traceable author statement PubMed 11752249. Source: SGD
Cellular_component	cytoplasm Inferred from direct assay PubMed 11914276. Source: SGD
Molecular_function	mRNA binding Inferred from direct assay PubMed 20844764. Source: SGD saccharopine dehydrogenase (NAD+, L-lysine-forming) activity Inferred from direct assay PubMed 17002315. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RSP5	P39940	3	EBI-10264,EBI-16219

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.4 Ref.5

Chain

2 – 373

372

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

PRO_0000199016

Sites

Active site

205

Ref.9

Amino acid modifications

Modified residue

N-acetylalanine; partial Ref.4

Experimental info

Sequence conflict

209

A → AL AA sequence Ref.6

Sequence conflict

309

A → V in CAA54551. Ref.1

Secondary structure

373

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P38998 [UniParc].

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

FASTA

373

41,465

        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' referencesShow '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. 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.

PIR

S48496.

RefSeq

NP_012300.3. NM_001179556.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2Q99	X-ray	1.64	A	1-373	[»]
2QRJ	X-ray	1.60	A	1-373	[»]
2QRK	X-ray	1.75	A	1-373	[»]
2QRL	X-ray	1.60	A	1-373	[»]
3UGK	X-ray	2.01	A	1-373	[»]
3UH1	X-ray	2.17	A	1-373	[»]
3UHA	X-ray	2.30	A/B	1-373	[»]

ProteinModelPortal

P38998.

SMR

P38998. Positions 3-373.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-5291N.

IntAct

P38998. 10 interactions.

MINT

MINT-524089.

STRING

4932.YIR034C.

Proteomic databases

PaxDb

P38998.

PeptideAtlas

P38998.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YIR034C; YIR034C; YIR034C.

GeneID

854852.

KEGG

sce:YIR034C.

Organism-specific databases

SGD

S000001473. LYS1.

Phylogenomic databases

eggNOG

NOG79735.

HOGENOM

HOG000143704.

K00290.

OMA

QFAHCYK.

OrthoDB

EOG408RHS.

Enzyme and pathway databases

BioCyc

YEAST:YIR034C-MONOMER.

SABIO-RK

P38998.

UniPathway

UPA00033; UER00034.

Gene expression databases

Genevestigator

P38998.

GermOnline

YIR034C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR007886. AlaDH/PNT_N.
IPR007698. AlaDH/PNT_NAD(H)-bd.
IPR027281. Lys1.
[Graphical view]

PANTHER

PTHR11133:SF4. PTHR11133:SF4. 1 hit.

Pfam

PF01262. AlaDh_PNT_C. 1 hit.
PF05222. AlaDh_PNT_N. 1 hit.
[Graphical view]

PIRSF

PIRSF018250. Saccharopine_DH_Lys. 1 hit.

SMART

SM01002. AlaDh_PNT_C. 1 hit.
SM01003. AlaDh_PNT_N. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P38998.

NextBio

977755.

Entry information

Entry name

LYS1_YEAST

Accession

Primary (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 status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal 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

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Sites

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents