SGPL_YEAST
ID SGPL_YEAST Reviewed; 589 AA.
AC Q05567; D6VSS3;
DT 24-OCT-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 161.
DE RecName: Full=Sphingosine-1-phosphate lyase {ECO:0000303|PubMed:9334171};
DE Short=S1PL {ECO:0000303|PubMed:9334171};
DE Short=SP-lyase {ECO:0000303|PubMed:9334171};
DE Short=ySPL {ECO:0000303|PubMed:9334171};
DE EC=4.1.2.- {ECO:0000269|PubMed:25345524};
DE EC=4.1.2.27 {ECO:0000269|PubMed:20696404, ECO:0000269|PubMed:25345524};
DE AltName: Full=Bestowed of sphingosine tolerance 1 {ECO:0000303|PubMed:9334171};
DE AltName: Full=Sphingosine-1-phosphate aldolase {ECO:0000303|PubMed:9334171};
GN Name=DPL1 {ECO:0000303|PubMed:20696404};
GN Synonyms=BST1 {ECO:0000303|PubMed:9334171}; OrderedLocusNames=YDR294C;
GN ORFNames=D9819.5;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=9334171; DOI=10.1074/jbc.272.42.26087;
RA Saba J.D., Nara F., Bielawska A., Garrett S., Hannun Y.A.;
RT "The BST1 gene of Saccharomyces cerevisiae is the sphingosine-1-phosphate
RT lyase.";
RL J. Biol. Chem. 272:26087-26090(1997).
RN [4]
RP CATALYTIC ACTIVITY.
RX PubMed=9464245; DOI=10.1006/bbrc.1997.7993;
RA Zhou J., Saba J.D.;
RT "Identification of the first mammalian sphingosine phosphate lyase gene and
RT its functional expression in yeast.";
RL Biochem. Biophys. Res. Commun. 242:502-507(1998).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=10329480; DOI=10.1006/mcbr.1999.0109;
RA Gottlieb D., Heideman W., Saba J.D.;
RT "The DPL1 gene is involved in mediating the response to nutrient
RT deprivation in Saccharomyces cerevisiae.";
RL Mol. Cell Biol. Res. Commun. 1:66-71(1999).
RN [6]
RP FUNCTION.
RX PubMed=11795842; DOI=10.1007/s00294-001-0259-6;
RA Zhang X., Skrzypek M.S., Lester R.L., Dickson R.C.;
RT "Elevation of endogenous sphingolipid long-chain base phosphates kills
RT Saccharomyces cerevisiae cells.";
RL Curr. Genet. 40:221-233(2001).
RN [7]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [8]
RP CATALYTIC ACTIVITY, TOPOLOGY, SUBCELLULAR LOCATION, AND MUTAGENESIS OF
RP 65-CYS--ASN-71 AND LYS-67.
RX PubMed=18487605; DOI=10.1074/jbc.m709753200;
RA Mukhopadhyay D., Howell K.S., Riezman H., Capitani G.;
RT "Identifying key residues of sphinganine-1-phosphate lyase for function in
RT vivo and in vitro.";
RL J. Biol. Chem. 283:20159-20169(2008).
RN [9]
RP FUNCTION, DISRUPTION PHENOTYPE, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=25345524; DOI=10.1038/ncomms6338;
RA Kondo N., Ohno Y., Yamagata M., Obara T., Seki N., Kitamura T.,
RA Naganuma T., Kihara A.;
RT "Identification of the phytosphingosine metabolic pathway leading to odd-
RT numbered fatty acids.";
RL Nat. Commun. 5:5338-5338(2014).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (3.15 ANGSTROMS) OF 103-589 IN COMPLEX WITH PYRIDOXAL
RP PHOSPHATE, CATALYTIC ACTIVITY, FUNCTION, COFACTOR, SUBUNIT, AND MUTAGENESIS
RP OF ALA-172; TYR-174; HIS-198; LYS-380; LYS-386 AND TYR-554.
RX PubMed=20696404; DOI=10.1016/j.str.2010.05.011;
RA Bourquin F., Riezman H., Capitani G., Grutter M.G.;
RT "Structure and function of sphingosine-1-phosphate lyase, a key enzyme of
RT sphingolipid metabolism.";
RL Structure 18:1054-1065(2010).
CC -!- FUNCTION: Sphingosine-1-phosphate lyase that cleaves phosphorylated
CC sphingoid bases (PSBs), such as sphingosine-1-phosphate, into fatty
CC aldehydes and phosphoethanolamine (PubMed:20696404, PubMed:25345524,
CC PubMed:9334171). Prefers C-16 dihydrosphingosine-l-phosphate (DHS-P) as
CC a substrate. Regulates intracellular levels of sphingolipid long-chain
CC base phosphates (LCBPs) (PubMed:11795842). Plays a role in the
CC regulation of global responses to nutrient deprivation in yeast
CC (PubMed:10329480). {ECO:0000269|PubMed:10329480,
CC ECO:0000269|PubMed:11795842, ECO:0000269|PubMed:20696404,
CC ECO:0000269|PubMed:25345524, ECO:0000269|PubMed:9334171}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=sphinganine 1-phosphate = hexadecanal + phosphoethanolamine;
CC Xref=Rhea:RHEA:18593, ChEBI:CHEBI:17600, ChEBI:CHEBI:57939,
CC ChEBI:CHEBI:58190; EC=4.1.2.27;
CC Evidence={ECO:0000269|PubMed:20696404, ECO:0000269|PubMed:25345524,
CC ECO:0000269|PubMed:9334171, ECO:0000269|PubMed:9464245};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:18594;
CC Evidence={ECO:0000269|PubMed:20696404, ECO:0000269|PubMed:25345524,
CC ECO:0000305|PubMed:9334171, ECO:0000305|PubMed:9464245};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(4R)-hydroxysphinganine 1-phosphate = (2R)-hydroxyhexadecanal
CC + phosphoethanolamine; Xref=Rhea:RHEA:55208, ChEBI:CHEBI:58190,
CC ChEBI:CHEBI:64795, ChEBI:CHEBI:138635;
CC Evidence={ECO:0000269|PubMed:18487605, ECO:0000269|PubMed:25345524};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:55209;
CC Evidence={ECO:0000269|PubMed:25345524, ECO:0000305|PubMed:18487605};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:20696404};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=19.6 uM for dihydrosphingosin 1-phosphate
CC {ECO:0000269|PubMed:25345524};
CC KM=10.6 uM for phytosphingosin 1-phosphate
CC {ECO:0000269|PubMed:25345524};
CC Vmax=28.3 nmol/min/ug enzyme toward dihydrosphingosin 1-phosphate
CC {ECO:0000269|PubMed:25345524};
CC Vmax=8.9 nmol/min/ug enzyme toward phytosphingosin 1-phosphate
CC {ECO:0000269|PubMed:25345524};
CC -!- PATHWAY: Lipid metabolism; sphingolipid metabolism.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:20696404}.
CC -!- INTERACTION:
CC Q05567; Q05567: DPL1; NbExp=3; IntAct=EBI-33743, EBI-33743;
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
CC {ECO:0000269|PubMed:18487605}; Single-pass type I membrane protein
CC {ECO:0000255}. Note=Localizes to the cortical and the perinuclear ER.
CC {ECO:0000269|PubMed:18487605}.
CC -!- PTM: Glycosylated. {ECO:0000269|PubMed:18487605}.
CC -!- DISRUPTION PHENOTYPE: Leads to the accumulation of endogenous
CC phosphorylated sphingoid bases, and exhibits unregulated proliferation
CC upon approach to stationary phase (PubMed:10329480). Causes a reduction
CC in total C15 and C17 phosphatidylcholine levels (PubMed:25345524).
CC {ECO:0000269|PubMed:10329480, ECO:0000269|PubMed:25345524}.
CC -!- MISCELLANEOUS: Present with 13100 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the group II decarboxylase family. Sphingosine-
CC 1-phosphate lyase subfamily. {ECO:0000305}.
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DR EMBL; U51031; AAB64470.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA12133.1; -; Genomic_DNA.
DR PIR; S70123; S70123.
DR RefSeq; NP_010580.1; NM_001180602.1.
DR PDB; 3MC6; X-ray; 3.15 A; A/C=103-589.
DR PDBsum; 3MC6; -.
DR AlphaFoldDB; Q05567; -.
DR SMR; Q05567; -.
DR BioGRID; 32346; 162.
DR DIP; DIP-49371N; -.
DR IntAct; Q05567; 2.
DR STRING; 4932.YDR294C; -.
DR SwissLipids; SLP:000000071; -.
DR SwissLipids; SLP:000000196; -.
DR iPTMnet; Q05567; -.
DR MaxQB; Q05567; -.
DR PaxDb; Q05567; -.
DR PRIDE; Q05567; -.
DR EnsemblFungi; YDR294C_mRNA; YDR294C; YDR294C.
DR GeneID; 851888; -.
DR KEGG; sce:YDR294C; -.
DR SGD; S000002702; DPL1.
DR VEuPathDB; FungiDB:YDR294C; -.
DR eggNOG; KOG1383; Eukaryota.
DR GeneTree; ENSGT00390000000046; -.
DR HOGENOM; CLU_028929_1_0_1; -.
DR InParanoid; Q05567; -.
DR OMA; FKDHQFT; -.
DR BioCyc; MetaCyc:YDR294C-MON; -.
DR BioCyc; YEAST:YDR294C-MON; -.
DR BRENDA; 4.1.2.27; 984.
DR Reactome; R-SCE-1660661; Sphingolipid de novo biosynthesis.
DR UniPathway; UPA00222; -.
DR EvolutionaryTrace; Q05567; -.
DR PRO; PR:Q05567; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; Q05567; protein.
DR GO; GO:0032541; C:cortical endoplasmic reticulum; IDA:SGD.
DR GO; GO:0005783; C:endoplasmic reticulum; HDA:SGD.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0097038; C:perinuclear endoplasmic reticulum; IDA:SGD.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR GO; GO:0008117; F:sphinganine-1-phosphate aldolase activity; IDA:SGD.
DR GO; GO:0019722; P:calcium-mediated signaling; IMP:SGD.
DR GO; GO:0019752; P:carboxylic acid metabolic process; IEA:InterPro.
DR GO; GO:0009267; P:cellular response to starvation; IMP:SGD.
DR GO; GO:0030149; P:sphingolipid catabolic process; IBA:GO_Central.
DR GO; GO:0006665; P:sphingolipid metabolic process; IMP:SGD.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR InterPro; IPR002129; PyrdxlP-dep_de-COase.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR Pfam; PF00282; Pyridoxal_deC; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Endoplasmic reticulum; Glycoprotein; Lipid metabolism; Lyase;
KW Membrane; Pyridoxal phosphate; Reference proteome; Sphingolipid metabolism;
KW Transmembrane; Transmembrane helix.
FT CHAIN 1..589
FT /note="Sphingosine-1-phosphate lyase"
FT /id="PRO_0000147018"
FT TOPO_DOM 1..58
FT /note="Lumenal"
FT /evidence="ECO:0000305"
FT TRANSMEM 59..76
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 77..589
FT /note="Cytoplasmic"
FT /evidence="ECO:0000305"
FT MOD_RES 380
FT /note="N6-(pyridoxal phosphate)lysine"
FT CARBOHYD 6
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT MUTAGEN 65..71
FT /note="CYKLISN->LYLLILL: In Dpl1CKSN_LLLL; impairs the
FT formation of higher oder oligomeric complexes and
FT consequently reduces catalytic activity."
FT /evidence="ECO:0000269|PubMed:18487605"
FT MUTAGEN 67
FT /note="K->L: Reduces catalytic activity."
FT /evidence="ECO:0000269|PubMed:18487605"
FT MUTAGEN 172
FT /note="A->P: Loss of enzyme activity."
FT /evidence="ECO:0000269|PubMed:20696404"
FT MUTAGEN 174
FT /note="Y->F: Mildly decreased enzyme activity."
FT /evidence="ECO:0000269|PubMed:20696404"
FT MUTAGEN 198
FT /note="H->A: Decreased enzyme activity."
FT /evidence="ECO:0000269|PubMed:20696404"
FT MUTAGEN 380
FT /note="K->A: Loss of enzyme activity."
FT /evidence="ECO:0000269|PubMed:20696404"
FT MUTAGEN 386
FT /note="K->A: Loss of enzyme activity."
FT /evidence="ECO:0000269|PubMed:20696404"
FT MUTAGEN 554
FT /note="Y->F: Decreased enzyme activity."
FT /evidence="ECO:0000269|PubMed:20696404"
FT HELIX 145..157
FT /evidence="ECO:0007829|PDB:3MC6"
FT HELIX 164..166
FT /evidence="ECO:0007829|PDB:3MC6"
FT STRAND 169..172
FT /evidence="ECO:0007829|PDB:3MC6"
FT HELIX 178..190
FT /evidence="ECO:0007829|PDB:3MC6"
FT TURN 199..201
FT /evidence="ECO:0007829|PDB:3MC6"
FT HELIX 203..219
FT /evidence="ECO:0007829|PDB:3MC6"
FT TURN 224..226
FT /evidence="ECO:0007829|PDB:3MC6"
FT STRAND 229..234
FT /evidence="ECO:0007829|PDB:3MC6"
FT HELIX 235..253
FT /evidence="ECO:0007829|PDB:3MC6"
FT STRAND 260..264
FT /evidence="ECO:0007829|PDB:3MC6"
FT HELIX 269..277
FT /evidence="ECO:0007829|PDB:3MC6"
FT STRAND 281..285
FT /evidence="ECO:0007829|PDB:3MC6"
FT TURN 289..291
FT /evidence="ECO:0007829|PDB:3MC6"
FT TURN 296..299
FT /evidence="ECO:0007829|PDB:3MC6"
FT HELIX 300..302
FT /evidence="ECO:0007829|PDB:3MC6"
FT STRAND 305..313
FT /evidence="ECO:0007829|PDB:3MC6"
FT TURN 317..319
FT /evidence="ECO:0007829|PDB:3MC6"
FT TURN 326..330
FT /evidence="ECO:0007829|PDB:3MC6"
FT HELIX 331..334
FT /evidence="ECO:0007829|PDB:3MC6"
FT STRAND 339..342
FT /evidence="ECO:0007829|PDB:3MC6"
FT TURN 343..346
FT /evidence="ECO:0007829|PDB:3MC6"
FT HELIX 347..350
FT /evidence="ECO:0007829|PDB:3MC6"
FT HELIX 351..353
FT /evidence="ECO:0007829|PDB:3MC6"
FT TURN 354..357
FT /evidence="ECO:0007829|PDB:3MC6"
FT STRAND 373..377
FT /evidence="ECO:0007829|PDB:3MC6"
FT TURN 378..382
FT /evidence="ECO:0007829|PDB:3MC6"
FT STRAND 389..392
FT /evidence="ECO:0007829|PDB:3MC6"
FT HELIX 396..399
FT /evidence="ECO:0007829|PDB:3MC6"
FT TURN 400..402
FT /evidence="ECO:0007829|PDB:3MC6"
FT STRAND 417..419
FT /evidence="ECO:0007829|PDB:3MC6"
FT HELIX 425..463
FT /evidence="ECO:0007829|PDB:3MC6"
FT STRAND 476..482
FT /evidence="ECO:0007829|PDB:3MC6"
FT TURN 484..487
FT /evidence="ECO:0007829|PDB:3MC6"
FT HELIX 488..496
FT /evidence="ECO:0007829|PDB:3MC6"
FT TURN 497..499
FT /evidence="ECO:0007829|PDB:3MC6"
FT STRAND 511..514
FT /evidence="ECO:0007829|PDB:3MC6"
FT TURN 517..520
FT /evidence="ECO:0007829|PDB:3MC6"
FT HELIX 523..537
FT /evidence="ECO:0007829|PDB:3MC6"
FT HELIX 567..575
FT /evidence="ECO:0007829|PDB:3MC6"
SQ SEQUENCE 589 AA; 65566 MW; 75FAF8182AF72266 CRC64;
MSGVSNKTVS INGWYGMPIH LLREEGDFAQ FMILTINELK IAIHGYLRNT PWYNMLKDYL
FVIFCYKLIS NFFYLLKVYG PVRLAVRTYE HSSRRLFRWL LDSPFLRGTV EKEVTKVKQS
IEDELIRSDS QLMNFPQLPS NGIPQDDVIE ELNKLNDLIP HTQWKEGKVS GAVYHGGDDL
IHLQTIAYEK YCVANQLHPD VFPAVRKMES EVVSMVLRMF NAPSDTGCGT TTSGGTESLL
LACLSAKMYA LHHRGITEPE IIAPVTAHAG FDKAAYYFGM KLRHVELDPT TYQVDLGKVK
KFINKNTILL VGSAPNFPHG IADDIEGLGK IAQKYKLPLH VDSCLGSFIV SFMEKAGYKN
LPLLDFRVPG VTSISCDTHK YGFAPKGSSV IMYRNSDLRM HQYYVNPAWT GGLYGSPTLA
GSRPGAIVVG CWATMVNMGE NGYIESCQEI VGAAMKFKKY IQENIPDLNI MGNPRYSVIS
FSSKTLNIHE LSDRLSKKGW HFNALQKPVA LHMAFTRLSA HVVDEICDIL RTTVQELKSE
SNSKPSPDGT SALYGVAGSV KTAGVADKLI VGFLDALYKL GPGEDTATK
