SIR4_YEAST
ID SIR4_YEAST Reviewed; 1358 AA.
AC P11978; D6VSK9;
DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1989, sequence version 1.
DT 03-AUG-2022, entry version 195.
DE RecName: Full=Regulatory protein SIR4;
DE AltName: Full=Silent information regulator 4;
GN Name=SIR4; Synonyms=ASD1, STE9, UTH2; OrderedLocusNames=YDR227W;
GN ORFNames=YD9934.12;
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 [GENOMIC DNA].
RX PubMed=3325825; DOI=10.1128/mcb.7.12.4441-4452.1987;
RA Marshall M., Mahoney D., Rose A., Hicks J.B., Broach J.R.;
RT "Functional domains of SIR4, a gene required for position effect regulation
RT in Saccharomyces cerevisiae.";
RL Mol. Cell. Biol. 7:4441-4452(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=7885847; DOI=10.1093/nar/23.3.507;
RA Davies C.J., Hutchison C.A. III;
RT "Insertion site specificity of the transposon Tn3.";
RL Nucleic Acids Res. 23:507-514(1995).
RN [3]
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 [4]
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 [5]
RP INTERACTION WITH RIS1.
RX PubMed=9271422; DOI=10.1128/mcb.17.9.5461;
RA Zhang Z., Buchman A.R.;
RT "Identification of a member of a DNA-dependent ATPase family that causes
RT interference with silencing.";
RL Mol. Cell. Biol. 17:5461-5472(1997).
RN [6]
RP FUNCTION, AND INTERACTION WITH UBP10.
RX PubMed=10490600; DOI=10.1128/mcb.19.10.6608;
RA Kahana A., Gottschling D.E.;
RT "DOT4 links silencing and cell growth in Saccharomyces cerevisiae.";
RL Mol. Cell. Biol. 19:6608-6620(1999).
RN [7]
RP REVIEW.
RX PubMed=11722841; DOI=10.1016/s0378-1119(01)00741-7;
RA Gasser S.M., Cockell M.M.;
RT "The molecular biology of the SIR proteins.";
RL Gene 279:1-16(2001).
RN [8]
RP INTERACTION WITH YKU80.
RX PubMed=14551211; DOI=10.1074/jbc.m306841200;
RA Roy R., Meier B., McAinsh A.D., Feldmann H.M., Jackson S.P.;
RT "Separation-of-function mutants of yeast Ku80 reveal a Yku80p-Sir4p
RT interaction involved in telomeric silencing.";
RL J. Biol. Chem. 279:86-94(2004).
RN [9]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-1128, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RX PubMed=15542864; DOI=10.1074/mcp.m400154-mcp200;
RA Denison C., Rudner A.D., Gerber S.A., Bakalarski C.E., Moazed D.,
RA Gygi S.P.;
RT "A proteomic strategy for gaining insights into protein sumoylation in
RT yeast.";
RL Mol. Cell. Proteomics 4:246-254(2005).
RN [10]
RP FUNCTION, AND INTERACTION WITH MPS3.
RX PubMed=18039933; DOI=10.1083/jcb.200706040;
RA Bupp J.M., Martin A.E., Stensrud E.S., Jaspersen S.L.;
RT "Telomere anchoring at the nuclear periphery requires the budding yeast
RT Sad1-UNC-84 domain protein Mps3.";
RL J. Cell Biol. 179:845-854(2007).
RN [11]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [12]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-692, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [13]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [14]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [15]
RP X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF 1271-1346.
RX PubMed=12791253; DOI=10.1016/s0969-2126(03)00093-5;
RA Chang J.F., Hall B.E., Tanny J.C., Moazed D., Filman D., Ellenberger T.;
RT "Structure of the coiled-coil dimerization motif of Sir4 and its
RT interaction with Sir3.";
RL Structure 11:637-649(2003).
RN [16]
RP INTERACTION WITH UBP10.
RX PubMed=26149687; DOI=10.1074/jbc.m115.650952;
RA Reed B.J., Locke M.N., Gardner R.G.;
RT "A conserved deubiquitinating enzyme uses intrinsically disordered regions
RT to scaffold multiple protein interaction sites.";
RL J. Biol. Chem. 290:20601-20612(2015).
CC -!- FUNCTION: The proteins SIR1 through SIR4 are required for
CC transcriptional repression of the silent mating type loci, HML and HMR
CC (PubMed:18039933). The proteins SIR2 through SIR4 repress mulitple loci
CC by modulating chromatin structure (PubMed:18039933). Involves the
CC compaction of chromatin fiber into a more condensed form
CC (PubMed:18039933). {ECO:0000269|PubMed:10490600,
CC ECO:0000269|PubMed:18039933}.
CC -!- SUBUNIT: Homodimer (PubMed:12791253). Interacts with MPS3
CC (PubMed:18039933). Interacts with RIS1 (PubMed:9271422). Interacts with
CC SIR1, SIR2 and SIR3 (PubMed:11722841). Interacts with YKU80
CC (PubMed:14551211). Interacts with UBP10 (PubMed:10490600,
CC PubMed:26149687). {ECO:0000269|PubMed:10490600,
CC ECO:0000269|PubMed:14551211, ECO:0000269|PubMed:18039933,
CC ECO:0000269|PubMed:26149687, ECO:0000269|PubMed:9271422,
CC ECO:0000303|PubMed:11722841}.
CC -!- INTERACTION:
CC P11978; P38181: NUP170; NbExp=3; IntAct=EBI-17237, EBI-11756;
CC P11978; P11938: RAP1; NbExp=4; IntAct=EBI-17237, EBI-14821;
CC P11978; P40161: RTT106; NbExp=2; IntAct=EBI-17237, EBI-29119;
CC P11978; P06700: SIR2; NbExp=7; IntAct=EBI-17237, EBI-17219;
CC P11978; P06701: SIR3; NbExp=8; IntAct=EBI-17237, EBI-17230;
CC P11978; Q04437: YKU80; NbExp=2; IntAct=EBI-17237, EBI-8224;
CC -!- SUBCELLULAR LOCATION: Nucleus.
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DR EMBL; M37249; AAA20881.1; -; Genomic_DNA.
DR EMBL; U13239; AAC33144.1; -; Genomic_DNA.
DR EMBL; Z48612; CAA88507.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA12069.1; -; Genomic_DNA.
DR PIR; A29360; A29360.
DR RefSeq; NP_010513.1; NM_001180535.1.
DR PDB; 1NYH; X-ray; 3.10 A; A=1198-1358.
DR PDB; 1PL5; X-ray; 2.50 A; A/S=1217-1358.
DR PDB; 4IAO; X-ray; 2.90 A; C/D=737-893.
DR PDB; 6QSZ; X-ray; 2.50 A; A/C/E/G/I/K/M/O=961-1085.
DR PDB; 6QTM; X-ray; 3.00 A; A/B/C=961-1085.
DR PDB; 6RR0; X-ray; 2.18 A; A/B/C/D/E/F/G=961-1085.
DR PDB; 6RRV; X-ray; 1.10 A; A=961-1085.
DR PDBsum; 1NYH; -.
DR PDBsum; 1PL5; -.
DR PDBsum; 4IAO; -.
DR PDBsum; 6QSZ; -.
DR PDBsum; 6QTM; -.
DR PDBsum; 6RR0; -.
DR PDBsum; 6RRV; -.
DR AlphaFoldDB; P11978; -.
DR SMR; P11978; -.
DR BioGRID; 32279; 133.
DR ComplexPortal; CPX-1811; Sir2-3-4 silent chromatin complex.
DR DIP; DIP-33N; -.
DR IntAct; P11978; 36.
DR MINT; P11978; -.
DR STRING; 4932.YDR227W; -.
DR iPTMnet; P11978; -.
DR MaxQB; P11978; -.
DR PaxDb; P11978; -.
DR PRIDE; P11978; -.
DR EnsemblFungi; YDR227W_mRNA; YDR227W; YDR227W.
DR GeneID; 851813; -.
DR KEGG; sce:YDR227W; -.
DR SGD; S000002635; SIR4.
DR VEuPathDB; FungiDB:YDR227W; -.
DR eggNOG; ENOG502S6NU; Eukaryota.
DR HOGENOM; CLU_257187_0_0_1; -.
DR InParanoid; P11978; -.
DR OMA; ETERNAM; -.
DR BioCyc; YEAST:G3O-29806-MON; -.
DR EvolutionaryTrace; P11978; -.
DR PRO; PR:P11978; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; P11978; protein.
DR GO; GO:0005677; C:chromatin silencing complex; IDA:SGD.
DR GO; GO:0000781; C:chromosome, telomeric region; IDA:SGD.
DR GO; GO:0003690; F:double-stranded DNA binding; IDA:SGD.
DR GO; GO:0060090; F:molecular adaptor activity; IMP:SGD.
DR GO; GO:0031491; F:nucleosome binding; IDA:SGD.
DR GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IMP:SGD.
DR GO; GO:0097695; P:establishment of protein-containing complex localization to telomere; IMP:SGD.
DR GO; GO:0031453; P:positive regulation of heterochromatin assembly; IMP:SGD.
DR GO; GO:0030466; P:silent mating-type cassette heterochromatin assembly; IMP:SGD.
DR GO; GO:0031509; P:subtelomeric heterochromatin assembly; IMP:SGD.
DR GO; GO:0034398; P:telomere tethering at nuclear periphery; IMP:SGD.
DR CDD; cd13746; Sir4p-SID_like; 1.
DR InterPro; IPR031556; SIR4_SID.
DR Pfam; PF16991; SIR4_SID; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Coiled coil; DNA-binding; Isopeptide bond; Nucleus;
KW Phosphoprotein; Reference proteome; Repressor; Transcription;
KW Transcription regulation; Ubl conjugation.
FT CHAIN 1..1358
FT /note="Regulatory protein SIR4"
FT /id="PRO_0000097769"
FT REGION 1..98
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 252..277
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 356..466
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 498..544
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 677..726
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 752..787
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 913..970
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 1271..1347
FT COMPBIAS 1..19
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 22..38
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 50..98
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 370..389
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 397..420
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 427..442
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 501..519
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 688..717
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 753..783
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 913..953
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 692
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT CROSSLNK 1128
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO)"
FT /evidence="ECO:0000269|PubMed:15542864"
FT VARIANT 994
FT /note="P -> L"
FT HELIX 808..821
FT /evidence="ECO:0007829|PDB:4IAO"
FT HELIX 829..837
FT /evidence="ECO:0007829|PDB:4IAO"
FT TURN 846..848
FT /evidence="ECO:0007829|PDB:4IAO"
FT TURN 854..857
FT /evidence="ECO:0007829|PDB:4IAO"
FT TURN 861..863
FT /evidence="ECO:0007829|PDB:4IAO"
FT HELIX 864..866
FT /evidence="ECO:0007829|PDB:4IAO"
FT HELIX 869..872
FT /evidence="ECO:0007829|PDB:4IAO"
FT STRAND 879..883
FT /evidence="ECO:0007829|PDB:4IAO"
FT HELIX 969..982
FT /evidence="ECO:0007829|PDB:6RRV"
FT STRAND 986..989
FT /evidence="ECO:0007829|PDB:6RRV"
FT HELIX 999..1018
FT /evidence="ECO:0007829|PDB:6RRV"
FT STRAND 1023..1026
FT /evidence="ECO:0007829|PDB:6RRV"
FT HELIX 1028..1030
FT /evidence="ECO:0007829|PDB:6RRV"
FT STRAND 1032..1038
FT /evidence="ECO:0007829|PDB:6RRV"
FT HELIX 1040..1042
FT /evidence="ECO:0007829|PDB:6RRV"
FT HELIX 1048..1057
FT /evidence="ECO:0007829|PDB:6RRV"
FT STRAND 1060..1062
FT /evidence="ECO:0007829|PDB:6RR0"
FT STRAND 1066..1069
FT /evidence="ECO:0007829|PDB:6RRV"
FT HELIX 1070..1079
FT /evidence="ECO:0007829|PDB:6RRV"
FT HELIX 1273..1342
FT /evidence="ECO:0007829|PDB:1PL5"
FT TURN 1343..1345
FT /evidence="ECO:0007829|PDB:1PL5"
SQ SEQUENCE 1358 AA; 152062 MW; 9C698765964F094E CRC64;
MPNDNKTPNR SSTPKFTKKP VTPNDKIPER EEKSNEVKTP KIPLFTFAKS KNYSRPSTAI
HTSPHQPSDV KPTSHKQLQQ PKSSPLKKNN YNSFPHSNLE KISNSKLLSL LRSKTSAGRI
ESNNPSHDAS RSLASFEQTA FSRHAQQQTS TFNSKPVRTI VPISTSQTNN SFLSGVKSLL
SEEKIRDYSK EILGINLANE QPVLEKPLKK GSADIGASVI SLTKDKSIRK DTVEEKKEEK
LNIGKNFAHS DSLSVPKVSA GDSGISPEES KARSPGIAKP NAIQTEVYGI NEESTNERLE
INQEKPVKLD ENSANSTVAS ALDTNGTSAT TETLTSKKIV PSPKKVAIDQ DKITLHDEKT
LAPSKHQPIT SEQKMKEDAD LKRMEILKSP HLSKSPADRP QGRRNSRNFS TRDEETTKLA
FLVEYEGQEN NYNSTSRSTE KKNDMNTSAK NKNGENKKIG KRPPEIMSTE AHVNKVTEET
TKQIQSVRID GRKVLQKVQG ESHIDSRNNT LNVTPSKRPQ LGEIPNPMKK HKPNEGRTPN
ISNGTINIQK KLEPKEIVRD ILHTKESSNE AKKTIQNPLN KSQNTALPST HKVTQKKDIK
IGTNDLFQVE SAPKISSEID RENVKSKDEP VSKAVESKSL LNLFSNVLKA PFIKSESKPF
SSDALSKEKA NFLETIASTE KPENKTDKVS LSQPVSASKH EYSDNFPVSL SQPSKKSFAN
HTEDEQIEKK KICRGRMNTI ITHPGKMELV YVSDSDDSSS DNDSLTDLES LSSGESNEIK
VTNDLDTSAE KDQIQAGKWF DPVLDWRKSD RELTKNILWR IADKTTYDKE TITDLIEQGI
PKHSYLSGNP LTSVTNDICS VENYETSSAF FYQQVHKKDR LQYLPLYAVS TFENTNNTEK
NDVTNKNINI GKHSQEQNSS SAKPSQIPTV SSPLGFEETK LSTTPTKSNR RVSHSDTNSS
KPKNTKENLS KSSWRQEWLA NLKLISVSLV DEFPSELSDS DRQIINEKMQ LLKDIFANNL
KSAISNNFRE SDIIILKGEI EDYPMSSEIK IYYNELQNKP DAKKARFWSF MKTQRFVSNM
GFDIQKSCEP VSISTSVKPH VVEPEHMADA KIMPKDILQI TKKPLMVKNV KPSSPPDVKS
LVQLSTMETK TLPEKKQFDS IFNSNKAKII PGNGKHASEN ISLSFSRPAS YGYFSVGKRV
PIVEDRRVKQ LDDITDSNTT EILTSVDVLG THSQTGTQQS NMYTSTQKTE LEIDNKDSVT
ECSKDMKEDG LSFVDIVLSK AASALDEKEK QLAVANEIIR SLSDEVMRNE IRITSLQGDL
TFTKKCLENA RSQISEKDAK INKLMEKDFQ VNKEIKPY
