LYS1 saccharopine dehydrogenase (NAD+, L-lysine-forming) [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: LYS1
Official Full Name: saccharopine dehydrogenase (NAD+, L-lysine-forming)
Primary source: SGD:S000001473
Locus tag: YIR034C
See related: AllianceGenome:SGD:S000001473; FungiDB:YIR034C; VEuPathDB:YIR034C
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Enables mRNA binding activity and saccharopine dehydrogenase (NAD+, L-lysine-forming) activity. Involved in lysine biosynthetic process. Acts upstream of or within protein import into peroxisome matrix. Located in cytoplasm. [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See LYS1 in Genome Data Viewer

Location:: chromosome: IX

Exon count:: 1

Sequence:: Chromosome: IX; NC_001141.2 (419615..420736, complement)

Chromosome IX - NC_001141.2 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001141.2

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

investigation of crystal structure and catalytic mechanism of LYS1: Data are consistent with role for K77 acting as base accepting proton from lysine prior to nucleophilic attack and with role for H96 acting as acid-base catalyst to form imine.
Title: Evidence in support of lysine 77 and histidine 96 as acid-base catalytic residues in saccharopine dehydrogenase from Saccharomyces cerevisiae.
A disulfide bond between cys-205 and cys-249, in the vicinity of the NAD-binding site, is observed in the apoenzyme, while a dithiol is observed in a structure with AMP bound, suggesting preferential binding of the dinucleotide to reduced enzyme.
Title: The oxidation state of active site thiols determines activity of saccharopine dehydrogenase at low pH.
In the direction of lysine formation, once NAD+ and saccharopine bind, a group with a pKa of 6.2 accepts a proton from the secondary amine of saccharopine as it is oxidized.
Title: A proposed proton shuttle mechanism for saccharopine dehydrogenase from Saccharomyces cerevisiae.

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Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info
enables saccharopine dehydrogenase (NAD+, L-lysine-forming) activity	IDA Inferred from Direct Assay more info	PubMed
enables saccharopine dehydrogenase (NAD+, L-lysine-forming) activity	IEA Inferred from Electronic Annotation more info
enables saccharopine dehydrogenase activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in lysine biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in lysine biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lysine biosynthetic process via aminoadipic acid	IBA Inferred from Biological aspect of Ancestor more info
involved_in lysine biosynthetic process via aminoadipic acid	IEA Inferred from Electronic Annotation more info
involved_in lysine metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within protein import into peroxisome matrix	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	HDA more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in peroxisome	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: saccharopine dehydrogenase (NAD+, L-lysine-forming)

NP_012300.3

EC 1.5.1.7

Saccharopine dehydrogenase (NAD+, L-lysine-forming); catalyzes the conversion of saccharopine to L-lysine, which is the final step in the lysine biosynthesis pathway; contains mRNA binding activity; required for targeting of Pls1p to the peroxisomal matrix in the absence of lysine

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001141.2 Reference assembly

Range

419615..420736 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001179556.3 → NP_012300.3 TPA: saccharopine dehydrogenase (NAD+, L-lysine-forming) [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_012300.3

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VVW5, P38998

UniProtKB/TrEMBL

A6ZVV4, B3LTH6, B5VKX1, C7GLS2, C8ZAT6, G2WFW2, N1P987

Conserved Domains (1) summary

cd12188
Location:4 → 365

SDH; Saccharopine Dehydrogenase NAD-binding and catalytic domains