P38999 (LYS9_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
EC=1.5.1.10

Alternative name(s):
Saccharopine reductase

Gene names

Name:	LYS9
Synonyms:	LYS13
Ordered Locus Names:	YNR050C
ORF Names:	N3461

Organism

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

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	446 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	N(6)-(L-1,3-dicarboxypropyl)-L-lysine + NADP+ + H2O = L-glutamate + (S)-2-amino-6-oxohexanoate + NADPH.
Pathway	Amino-acid biosynthesis; L-lysine biosynthesis via AAA pathway; L-lysine from L-alpha-aminoadipate (fungal route): step 2/3.
Subunit structure	Interacts with TRM112. Ref.7
Miscellaneous	Present with 57500 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the saccharopine dehydrogenase family.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Lysine biosynthesis
Ligand	NADP
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	lysine biosynthetic process via aminoadipic acid Inferred from mutant phenotype PubMed 6429126. Source: SGD
Cellular_component	cytoplasm Inferred from direct assay PubMed 11914276PubMed 14562095. Source: SGD
Molecular_function	nucleotide binding Inferred from electronic annotation. Source: InterPro saccharopine dehydrogenase (NADP+, L-glutamate-forming) activity Inferred from direct assay PubMed 18416559. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		1	EBI-10294,EBI-10294

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 446

446

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

PRO_0000212839

Experimental info

Sequence conflict

393

1

A → T in AAT93229. Ref.4

Secondary structure

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446

Helix Strand Turn

Details...

Beta strand

3 – 8

6

Helix

14 – 22

9

Beta strand

27 – 35

9

Helix

36 – 43

8

Turn

44 – 47

4

Beta strand

49 – 52

4

Helix

58 – 66

9

Beta strand

68 – 73

6

Helix

77 – 79

3

Helix

80 – 90

11

Beta strand

93 – 96

4

Helix

102 – 114

13

Beta strand

117 – 119

3

Turn

124 – 126

3

Helix

128 – 142

15

Beta strand

146 – 158

13

Helix

160 – 162

3

Beta strand

171 – 173

3

Helix

176 – 180

5

Helix

181 – 183

3

Beta strand

186 – 190

5

Beta strand

193 – 197

5

Turn

199 – 201

3

Helix

202 – 205

4

Beta strand

217 – 221

5

Helix

228 – 231

4

Beta strand

238 – 247

10

Helix

250 – 259

10

Turn

260 – 263

4

Helix

269 – 271

3

Helix

277 – 285

9

Beta strand

288 – 291

4

Helix

292 – 300

9

Helix

308 – 320

13

Turn

321 – 324

4

Helix

335 – 346

12

Beta strand

355 – 366

12

Beta strand

372 – 382

11

Helix

390 – 407

18

Beta strand

414 – 417

4

Helix

422 – 436

15

Beta strand

441 – 444

4

Sequences

	Sequence		Length	Mass (Da)
	P38999 [UniParc]. Last modified February 1, 1995. Version 1. Checksum: 1EC4CE1CE3BCD916	FASTA	446	48,918
	10 20 30 40 50 60 MGKNVLLLGS GFVAQPVIDT LAANDDINVT VACRTLANAQ ALAKPSGSKA ISLDVTDDSA 70 80 90 100 110 120 LDKVLADNDV VISLIPYTFH PNVVKSAIRT KTDVVTSSYI SPALRELEPE IVKAGITVMN 130 140 150 160 170 180 EIGLDPGIDH LYAVKTIDEV HRAGGKLKSF LSYCGGLPAP EDSDNPLGYK FSWSSRGVLL 190 200 210 220 230 240 ALRNSAKYWK DGKIETVSSE DLMATAKPYF IYPGYAFVCY PNRDSTLFKD LYHIPEAETV 250 260 270 280 290 300 IRGTLRYQGF PEFVKALVDM GMLKDDANEI FSKPIAWNEA LKQYLGAKST SKEDLIASID 310 320 330 340 350 360 SKATWKDDED RERILSGFAW LGLFSDAKIT PRGNALDTLC ARLEELMQYE DNERDMVVLQ 370 380 390 400 410 420 HKFGIEWADG TTETRTSTLV DYGKVGGYSS MAATVGYPVA IATKFVLDGT IKGPGLLAPY 430 440 SPEINDPIMK ELKDKYGIYL KEKTVA

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: 1278B.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications." Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J. , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J. Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	"Protein expression during exponential growth in 0.7 M NaCl medium of Saccharomyces cerevisiae." Norbeck J., Blomberg A. FEMS Microbiol. Lett. 137:1-8(1996) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 314-324. Strain: ATCC 38531 / Y41.
[6]	"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].
[7]	"Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA." Purushothaman S.K., Bujnicki J.M., Grosjean H., Lapeyre B. Mol. Cell. Biol. 25:4359-4370(2005) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH TRM112.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X77363 Genomic DNA. Translation: CAA54552.1.
Z71665 Genomic DNA. Translation: CAA96331.1.
AY693210 Genomic DNA. Translation: AAT93229.1.
BK006947 Genomic DNA. Translation: DAA10591.1.

PIR

S41937.

RefSeq

NP_014448.1. NM_001183227.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2AXQ	X-ray	1.70	A	1-446	[»]

ProteinModelPortal

P38999.

SMR

P38999. Positions 2-446.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-776N.

IntAct

P38999. 8 interactions.

MINT

MINT-425978.

STRING

4932.YNR050C.

Proteomic databases

PaxDb

P38999.

PeptideAtlas

P38999.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YNR050C; YNR050C; YNR050C.

GeneID

855786.

KEGG

sce:YNR050C.

Organism-specific databases

CYGD

YNR050c.

SGD

S000005333. LYS9.

Phylogenomic databases

eggNOG

COG1748.

GeneTree

ENSGT00390000013249.

HOGENOM

HOG000023158.

KO

K00293.

OMA

VTVACRT.

OrthoDB

EOG4STWD0.

Enzyme and pathway databases

UniPathway

UPA00033; UER00033.

Gene expression databases

Genevestigator

P38999.

GermOnline

YNR050C. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

3.40.50.720. 1 hit.

InterPro

IPR016040. NAD(P)-bd_dom.
IPR005097. Saccharopine_DH/HSpermid_syn.
[Graphical view]

Pfam

PF03435. Saccharop_dh. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P38999.

NextBio

980265.

Entry information

Entry name

LYS9_YEAST

Accession

Primary (citable) accession number: P38999
Secondary accession number(s): D6W1M5, E9P930

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	April 3, 2013
This is version 115 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program