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Protein

Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]

Gene

LYS9

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

N(6)-(L-1,3-dicarboxypropyl)-L-lysine + NADP+ + H2O = L-glutamate + (S)-2-amino-6-oxohexanoate + NADPH.

Pathwayi: L-lysine biosynthesis via AAA pathway

This protein is involved in step 2 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.

GO - Molecular functioni

  • saccharopine dehydrogenase (NADP+, L-glutamate-forming) activity Source: SGD

GO - Biological processi

  • generation of precursor metabolites and energy Source: GO_Central
  • 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

NADP

Enzyme and pathway databases

BioCyciYEAST:MONOMER3O-363.
ReactomeiR-SCE-71064. Lysine catabolism.
UniPathwayiUPA00033; UER00033.

Names & Taxonomyi

Protein namesi
Recommended name:
Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] (EC:1.5.1.10)
Alternative name(s):
Saccharopine reductase
Gene namesi
Name:LYS9
Synonyms:LYS13
Ordered Locus Names:YNR050C
ORF Names:N3461
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNR050C.
SGDiS000005333. LYS9.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002128391 – 446Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]Add BLAST446

Proteomic databases

MaxQBiP38999.
PRIDEiP38999.

PTM databases

iPTMnetiP38999.

Interactioni

Subunit structurei

Interacts with TRM112.1 Publication

Protein-protein interaction databases

BioGridi35875. 17 interactors.
DIPiDIP-776N.
IntActiP38999. 9 interactors.
MINTiMINT-425978.

Structurei

Secondary structure

1446
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 8Combined sources6
Helixi14 – 22Combined sources9
Beta strandi27 – 35Combined sources9
Helixi36 – 43Combined sources8
Turni44 – 47Combined sources4
Beta strandi49 – 52Combined sources4
Helixi58 – 66Combined sources9
Beta strandi68 – 73Combined sources6
Helixi77 – 79Combined sources3
Helixi80 – 90Combined sources11
Beta strandi93 – 96Combined sources4
Helixi102 – 114Combined sources13
Beta strandi117 – 119Combined sources3
Turni124 – 126Combined sources3
Helixi128 – 142Combined sources15
Beta strandi146 – 158Combined sources13
Helixi160 – 162Combined sources3
Beta strandi171 – 173Combined sources3
Helixi176 – 180Combined sources5
Helixi181 – 183Combined sources3
Beta strandi186 – 190Combined sources5
Beta strandi193 – 197Combined sources5
Turni199 – 201Combined sources3
Helixi202 – 205Combined sources4
Beta strandi217 – 221Combined sources5
Helixi228 – 231Combined sources4
Beta strandi238 – 247Combined sources10
Helixi250 – 259Combined sources10
Turni260 – 263Combined sources4
Helixi269 – 271Combined sources3
Helixi277 – 285Combined sources9
Beta strandi288 – 291Combined sources4
Helixi292 – 300Combined sources9
Helixi308 – 320Combined sources13
Turni321 – 324Combined sources4
Helixi335 – 346Combined sources12
Beta strandi355 – 366Combined sources12
Beta strandi372 – 382Combined sources11
Helixi390 – 407Combined sources18
Beta strandi414 – 417Combined sources4
Helixi422 – 436Combined sources15
Beta strandi441 – 444Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2AXQX-ray1.70A1-446[»]
ProteinModelPortaliP38999.
SMRiP38999.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP38999.

Family & Domainsi

Sequence similaritiesi

Belongs to the saccharopine dehydrogenase family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000013249.
HOGENOMiHOG000023158.
InParanoidiP38999.
KOiK00293.
OMAiWNYKFTW.
OrthoDBiEOG092C2J3O.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
InterProiIPR016040. NAD(P)-bd_dom.
IPR032095. Sacchrp_dh_C.
IPR005097. Sacchrp_dh_NADP.
[Graphical view]
PfamiPF16653. Sacchrp_dh_C. 1 hit.
PF03435. Sacchrp_dh_NADP. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.

Sequencei

Sequence statusi: Complete.

P38999-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGKNVLLLGS GFVAQPVIDT LAANDDINVT VACRTLANAQ ALAKPSGSKA
60 70 80 90 100
ISLDVTDDSA LDKVLADNDV VISLIPYTFH PNVVKSAIRT KTDVVTSSYI
110 120 130 140 150
SPALRELEPE IVKAGITVMN EIGLDPGIDH LYAVKTIDEV HRAGGKLKSF
160 170 180 190 200
LSYCGGLPAP EDSDNPLGYK FSWSSRGVLL ALRNSAKYWK DGKIETVSSE
210 220 230 240 250
DLMATAKPYF IYPGYAFVCY PNRDSTLFKD LYHIPEAETV IRGTLRYQGF
260 270 280 290 300
PEFVKALVDM GMLKDDANEI FSKPIAWNEA LKQYLGAKST SKEDLIASID
310 320 330 340 350
SKATWKDDED RERILSGFAW LGLFSDAKIT PRGNALDTLC ARLEELMQYE
360 370 380 390 400
DNERDMVVLQ HKFGIEWADG TTETRTSTLV DYGKVGGYSS MAATVGYPVA
410 420 430 440
IATKFVLDGT IKGPGLLAPY SPEINDPIMK ELKDKYGIYL KEKTVA
Length:446
Mass (Da):48,918
Last modified:February 1, 1995 - v1
Checksum:i1EC4CE1CE3BCD916
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti393A → T in AAT93229 (PubMed:17322287).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X77363 Genomic DNA. Translation: CAA54552.1.
Z71665 Genomic DNA. Translation: CAA96331.1.
AY693210 Genomic DNA. Translation: AAT93229.1.
BK006947 Genomic DNA. Translation: DAA10591.1.
PIRiS41937.
RefSeqiNP_014448.1. NM_001183227.1.

Genome annotation databases

EnsemblFungiiYNR050C; YNR050C; YNR050C.
GeneIDi855786.
KEGGisce:YNR050C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X77363 Genomic DNA. Translation: CAA54552.1.
Z71665 Genomic DNA. Translation: CAA96331.1.
AY693210 Genomic DNA. Translation: AAT93229.1.
BK006947 Genomic DNA. Translation: DAA10591.1.
PIRiS41937.
RefSeqiNP_014448.1. NM_001183227.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2AXQX-ray1.70A1-446[»]
ProteinModelPortaliP38999.
SMRiP38999.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35875. 17 interactors.
DIPiDIP-776N.
IntActiP38999. 9 interactors.
MINTiMINT-425978.

PTM databases

iPTMnetiP38999.

Proteomic databases

MaxQBiP38999.
PRIDEiP38999.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNR050C; YNR050C; YNR050C.
GeneIDi855786.
KEGGisce:YNR050C.

Organism-specific databases

EuPathDBiFungiDB:YNR050C.
SGDiS000005333. LYS9.

Phylogenomic databases

GeneTreeiENSGT00390000013249.
HOGENOMiHOG000023158.
InParanoidiP38999.
KOiK00293.
OMAiWNYKFTW.
OrthoDBiEOG092C2J3O.

Enzyme and pathway databases

UniPathwayiUPA00033; UER00033.
BioCyciYEAST:MONOMER3O-363.
ReactomeiR-SCE-71064. Lysine catabolism.

Miscellaneous databases

EvolutionaryTraceiP38999.
PROiP38999.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
InterProiIPR016040. NAD(P)-bd_dom.
IPR032095. Sacchrp_dh_C.
IPR005097. Sacchrp_dh_NADP.
[Graphical view]
PfamiPF16653. Sacchrp_dh_C. 1 hit.
PF03435. Sacchrp_dh_NADP. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiLYS9_YEAST
AccessioniPrimary (citable) accession number: P38999
Secondary accession number(s): D6W1M5, E9P930
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: November 30, 2016
This is version 144 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 57500 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 XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: 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.