RPN11_YEAST
ID RPN11_YEAST Reviewed; 306 AA.
AC P43588; D6VTN4; Q8J0T5;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 1.
DT 03-AUG-2022, entry version 196.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase RPN11;
DE EC=3.4.19.12;
DE AltName: Full=26S proteasome regulatory subunit RPN11;
DE AltName: Full=Protein MPR1;
GN Name=RPN11; Synonyms=MPR1; OrderedLocusNames=YFR004W;
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].
RC STRAIN=S288c / GRF88;
RX PubMed=7628709; DOI=10.1016/0378-1119(95)00212-o;
RA Rinaldi T., Bolotin-Fukuhara M., Frontali L.;
RT "A Saccharomyces cerevisiae gene essential for viability has been conserved
RT in evolution.";
RL Gene 160:135-136(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 2601 / CBS 679 / DSM 3774 / NRRL Y-53;
RA Ambroggio X.I., Rees D.C., Deshaies R.J.;
RT "A putative naturally occurring allele of RPN11.";
RL Submitted (SEP-2002) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7670463; DOI=10.1038/ng0795-261;
RA Murakami Y., Naitou M., Hagiwara H., Shibata T., Ozawa M., Sasanuma S.,
RA Sasanuma M., Tsuchiya Y., Soeda E., Yokoyama K., Yamazaki M., Tashiro H.,
RA Eki T.;
RT "Analysis of the nucleotide sequence of chromosome VI from Saccharomyces
RT cerevisiae.";
RL Nat. Genet. 10:261-268(1995).
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [6]
RP PROTEIN SEQUENCE OF 1-8, AND ACETYLATION AT MET-1.
RX PubMed=12504901; DOI=10.1016/s0003-9861(02)00639-2;
RA Kimura Y., Saeki Y., Yokosawa H., Polevoda B., Sherman F., Hirano H.;
RT "N-terminal modifications of the 19S regulatory particle subunits of the
RT yeast proteasome.";
RL Arch. Biochem. Biophys. 409:341-348(2003).
RN [7]
RP FUNCTION, AND MUTAGENESIS OF HIS-109 AND HIS-111.
RX PubMed=12183636; DOI=10.1126/science.1075898;
RA Verma R., Aravind L., Oania R., McDonald W.H., Yates J.R., Koonin E.V.,
RA Deshaies R.J.;
RT "Role of Rpn11 metalloprotease in deubiquitination and degradation by the
RT 26S proteasome.";
RL Science 298:611-615(2002).
RN [8]
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 [9]
RP FUNCTION, AND INTERACTION WITH STS1.
RX PubMed=21075847; DOI=10.1074/jbc.m110.135863;
RA Chen L., Romero L., Chuang S.M., Tournier V., Joshi K.K., Lee J.A.,
RA Kovvali G., Madura K.;
RT "Sts1 plays a key role in targeting proteasomes to the nucleus.";
RL J. Biol. Chem. 286:3104-3118(2011).
RN [10]
RP STRUCTURE BY ELECTRON MICROSCOPY (7.4 ANGSTROMS) OF THE 26S PROTEASOME.
RX PubMed=22927375; DOI=10.1073/pnas.1213333109;
RA Beck F., Unverdorben P., Bohn S., Schweitzer A., Pfeifer G., Sakata E.,
RA Nickell S., Plitzko J.M., Villa E., Baumeister W., Forster F.;
RT "Near-atomic resolution structural model of the yeast 26S proteasome.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:14870-14875(2012).
RN [11]
RP STRUCTURE BY ELECTRON MICROSCOPY (9.80 ANGSTROMS), AND IDENTIFICATION IN
RP THE 26S PROTEASOME COMPLEX.
RX PubMed=23589842; DOI=10.1073/pnas.1305782110;
RA Sledz P., Unverdorben P., Beck F., Pfeifer G., Schweitzer A., Forster F.,
RA Baumeister W.;
RT "Structure of the 26S proteasome with ATP-gammaS bound provides insights
RT into the mechanism of nucleotide-dependent substrate translocation.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:7264-7269(2013).
RN [12]
RP STRUCTURE BY ELECTRON MICROSCOPY (9.80 ANGSTROMS), AND IDENTIFICATION IN
RP THE 26S PROTEASOME COMPLEX.
RX PubMed=23911091; DOI=10.1016/j.str.2013.06.023;
RA Estrin E., Lopez-Blanco J.R., Chacon P., Martin A.;
RT "Formation of an intricate helical bundle dictates the assembly of the 26S
RT proteasome lid.";
RL Structure 21:1624-1635(2013).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 2-239 IN COMPLEX WITH RPN8, AND
RP FUNCTION.
RX PubMed=24463465; DOI=10.1038/nsmb.2771;
RA Worden E.J., Padovani C., Martin A.;
RT "Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate
RT deubiquitination during proteasomal degradation.";
RL Nat. Struct. Mol. Biol. 21:220-227(2014).
CC -!- FUNCTION: Component of the lid subcomplex of the 26S proteasome, a
CC multiprotein complex involved in the ATP-dependent degradation of
CC ubiquitinated proteins. RPN11 is the only catalytically active member
CC of the lid and serves as the essential deubiquitinase of the
CC proteasome. {ECO:0000269|PubMed:12183636, ECO:0000269|PubMed:21075847,
CC ECO:0000269|PubMed:24463465}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Thiol-dependent hydrolysis of ester, thioester, amide, peptide
CC and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-
CC residue protein attached to proteins as an intracellular targeting
CC signal).; EC=3.4.19.12;
CC -!- SUBUNIT: Component of the lid subcomplex of the 19S proteasome
CC regulatory particle complex (also named PA700 complex). The 26S
CC proteasome consists of a 20S proteasome core and two 19S regulatory
CC subunits. Interacts directly with RPN8 and STS1.
CC {ECO:0000269|PubMed:21075847, ECO:0000269|PubMed:23589842,
CC ECO:0000269|PubMed:23911091, ECO:0000269|PubMed:24463465}.
CC -!- INTERACTION:
CC P43588; Q12250: RPN5; NbExp=7; IntAct=EBI-11219, EBI-15935;
CC P43588; Q08723: RPN8; NbExp=9; IntAct=EBI-11219, EBI-36176;
CC P43588; Q04062: RPN9; NbExp=5; IntAct=EBI-11219, EBI-15944;
CC P43588; P33299: RPT1; NbExp=3; IntAct=EBI-11219, EBI-13910;
CC P43588; P40327: RPT2; NbExp=2; IntAct=EBI-11219, EBI-13901;
CC P43588; P33298: RPT3; NbExp=3; IntAct=EBI-11219, EBI-13905;
CC P43588; P53549: RPT4; NbExp=3; IntAct=EBI-11219, EBI-18520;
CC P43588; Q01939: RPT6; NbExp=2; IntAct=EBI-11219, EBI-13914;
CC -!- DOMAIN: The JAMM motif is required for the deubiquitination and
CC degradation of ubiquitinated substrates. {ECO:0000269|PubMed:12183636}.
CC -!- PTM: N-acetylated by NAT3. {ECO:0000269|PubMed:12504901}.
CC -!- MISCELLANEOUS: Present with 16400 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the peptidase M67A family. {ECO:0000305}.
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DR EMBL; X79561; CAA56098.1; -; Genomic_DNA.
DR EMBL; AY152546; AAN77865.1; -; Genomic_DNA.
DR EMBL; D50617; BAA09243.1; -; Genomic_DNA.
DR EMBL; AY692755; AAT92774.1; -; Genomic_DNA.
DR EMBL; BK006940; DAA12444.1; -; Genomic_DNA.
DR PIR; S56259; S56259.
DR RefSeq; NP_116659.1; NM_001179969.1.
DR PDB; 3J47; EM; -; V=230-298.
DR PDB; 3JCK; EM; 3.50 A; G=1-306.
DR PDB; 3JCO; EM; 4.80 A; V=1-306.
DR PDB; 3JCP; EM; 4.60 A; V=1-306.
DR PDB; 4CR2; EM; 7.70 A; V=1-306.
DR PDB; 4CR3; EM; 9.30 A; V=1-306.
DR PDB; 4CR4; EM; 8.80 A; V=1-306.
DR PDB; 4O8X; X-ray; 1.99 A; B=2-239.
DR PDB; 4O8Y; X-ray; 1.95 A; B=2-239.
DR PDB; 4OCL; X-ray; 2.40 A; B/E=1-220.
DR PDB; 4OCM; X-ray; 1.99 A; B/E=1-220.
DR PDB; 4OCN; X-ray; 2.25 A; B/E=1-220.
DR PDB; 4OWP; X-ray; 2.35 A; B=2-229.
DR PDB; 5A5B; EM; 9.50 A; V=1-306.
DR PDB; 5MPB; EM; 7.80 A; V=1-306.
DR PDB; 5MPC; EM; 7.70 A; V=1-306.
DR PDB; 5MPD; EM; 4.10 A; V=1-306.
DR PDB; 5MPE; EM; 4.50 A; V=1-306.
DR PDB; 5U4P; X-ray; 2.50 A; B=2-219.
DR PDB; 5W83; X-ray; 1.55 A; B=1-222.
DR PDB; 5WVI; EM; 6.30 A; V=1-306.
DR PDB; 5WVK; EM; 4.20 A; V=1-306.
DR PDB; 6EF3; EM; 4.17 A; r=1-306.
DR PDB; 6FVT; EM; 4.10 A; V=18-306.
DR PDB; 6FVU; EM; 4.50 A; V=18-306.
DR PDB; 6FVV; EM; 5.40 A; V=18-306.
DR PDB; 6FVW; EM; 4.50 A; V=18-306.
DR PDB; 6FVX; EM; 4.90 A; V=18-306.
DR PDB; 6FVY; EM; 6.10 A; V=18-306.
DR PDB; 6J2C; EM; 7.00 A; V=1-306.
DR PDB; 6J2N; EM; 7.50 A; V=1-306.
DR PDB; 6J2Q; EM; 3.80 A; V=1-306.
DR PDB; 6J2X; EM; 3.80 A; V=1-306.
DR PDB; 6J30; EM; 4.50 A; V=1-306.
DR PDB; 7QO3; EM; 6.10 A; V=1-306.
DR PDB; 7QO5; EM; 6.00 A; V=1-306.
DR PDBsum; 3J47; -.
DR PDBsum; 3JCK; -.
DR PDBsum; 3JCO; -.
DR PDBsum; 3JCP; -.
DR PDBsum; 4CR2; -.
DR PDBsum; 4CR3; -.
DR PDBsum; 4CR4; -.
DR PDBsum; 4O8X; -.
DR PDBsum; 4O8Y; -.
DR PDBsum; 4OCL; -.
DR PDBsum; 4OCM; -.
DR PDBsum; 4OCN; -.
DR PDBsum; 4OWP; -.
DR PDBsum; 5A5B; -.
DR PDBsum; 5MPB; -.
DR PDBsum; 5MPC; -.
DR PDBsum; 5MPD; -.
DR PDBsum; 5MPE; -.
DR PDBsum; 5U4P; -.
DR PDBsum; 5W83; -.
DR PDBsum; 5WVI; -.
DR PDBsum; 5WVK; -.
DR PDBsum; 6EF3; -.
DR PDBsum; 6FVT; -.
DR PDBsum; 6FVU; -.
DR PDBsum; 6FVV; -.
DR PDBsum; 6FVW; -.
DR PDBsum; 6FVX; -.
DR PDBsum; 6FVY; -.
DR PDBsum; 6J2C; -.
DR PDBsum; 6J2N; -.
DR PDBsum; 6J2Q; -.
DR PDBsum; 6J2X; -.
DR PDBsum; 6J30; -.
DR PDBsum; 7QO3; -.
DR PDBsum; 7QO5; -.
DR AlphaFoldDB; P43588; -.
DR SMR; P43588; -.
DR BioGRID; 31152; 1230.
DR ComplexPortal; CPX-2262; 26S Proteasome complex.
DR DIP; DIP-1573N; -.
DR IntAct; P43588; 37.
DR MINT; P43588; -.
DR STRING; 4932.YFR004W; -.
DR MEROPS; M67.001; -.
DR iPTMnet; P43588; -.
DR MaxQB; P43588; -.
DR PaxDb; P43588; -.
DR PRIDE; P43588; -.
DR ABCD; P43588; 1 sequenced antibody.
DR EnsemblFungi; YFR004W_mRNA; YFR004W; YFR004W.
DR GeneID; 850554; -.
DR KEGG; sce:YFR004W; -.
DR SGD; S000001900; RPN11.
DR VEuPathDB; FungiDB:YFR004W; -.
DR eggNOG; KOG1555; Eukaryota.
DR GeneTree; ENSGT00730000111116; -.
DR HOGENOM; CLU_052991_0_1_1; -.
DR InParanoid; P43588; -.
DR OMA; VFQTRMM; -.
DR BioCyc; YEAST:G3O-30457-MON; -.
DR Reactome; R-SCE-1236978; Cross-presentation of soluble exogenous antigens (endosomes).
DR Reactome; R-SCE-382556; ABC-family proteins mediated transport.
DR Reactome; R-SCE-5668541; TNFR2 non-canonical NF-kB pathway.
DR Reactome; R-SCE-5687128; MAPK6/MAPK4 signaling.
DR Reactome; R-SCE-5689880; Ub-specific processing proteases.
DR Reactome; R-SCE-5689901; Metalloprotease DUBs.
DR Reactome; R-SCE-6798695; Neutrophil degranulation.
DR Reactome; R-SCE-68949; Orc1 removal from chromatin.
DR Reactome; R-SCE-69017; CDK-mediated phosphorylation and removal of Cdc6.
DR Reactome; R-SCE-69601; Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
DR Reactome; R-SCE-75815; Ubiquitin-dependent degradation of Cyclin D.
DR Reactome; R-SCE-8854050; FBXL7 down-regulates AURKA during mitotic entry and in early mitosis.
DR Reactome; R-SCE-8948751; Regulation of PTEN stability and activity.
DR Reactome; R-SCE-8951664; Neddylation.
DR Reactome; R-SCE-9755511; KEAP1-NFE2L2 pathway.
DR Reactome; R-SCE-983168; Antigen processing: Ubiquitination & Proteasome degradation.
DR PRO; PR:P43588; -.
DR Proteomes; UP000002311; Chromosome VI.
DR RNAct; P43588; protein.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0005739; C:mitochondrion; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0000502; C:proteasome complex; IPI:ComplexPortal.
DR GO; GO:0008541; C:proteasome regulatory particle, lid subcomplex; IDA:SGD.
DR GO; GO:0034515; C:proteasome storage granule; IDA:SGD.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IEA:UniProtKB-EC.
DR GO; GO:0070122; F:isopeptidase activity; IEA:InterPro.
DR GO; GO:0061578; F:Lys63-specific deubiquitinase activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0140492; F:metal-dependent deubiquitinase activity; IEA:InterPro.
DR GO; GO:0008237; F:metallopeptidase activity; ISS:SGD.
DR GO; GO:0070628; F:proteasome binding; IBA:GO_Central.
DR GO; GO:0000266; P:mitochondrial fission; IMP:SGD.
DR GO; GO:0016559; P:peroxisome fission; IMP:SGD.
DR GO; GO:0043248; P:proteasome assembly; IMP:SGD.
DR GO; GO:1902906; P:proteasome storage granule assembly; IMP:SGD.
DR GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IDA:ComplexPortal.
DR GO; GO:0016579; P:protein deubiquitination; IDA:SGD.
DR InterPro; IPR000555; JAMM/MPN+_dom.
DR InterPro; IPR037518; MPN.
DR InterPro; IPR035299; PSMD14.
DR InterPro; IPR024969; Rpn11/EIF3F_C.
DR PANTHER; PTHR10410:SF22; PTHR10410:SF22; 1.
DR Pfam; PF01398; JAB; 1.
DR Pfam; PF13012; MitMem_reg; 1.
DR SMART; SM00232; JAB_MPN; 1.
DR PROSITE; PS50249; MPN; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Direct protein sequencing; Hydrolase;
KW Metal-binding; Metalloprotease; Protease; Proteasome; Reference proteome;
KW Thiol protease; Ubl conjugation pathway; Zinc.
FT CHAIN 1..306
FT /note="Ubiquitin carboxyl-terminal hydrolase RPN11"
FT /id="PRO_0000213960"
FT DOMAIN 27..162
FT /note="MPN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT REGION 1..20
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 109..122
FT /note="JAMM motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT BINDING 109
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT BINDING 111
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT BINDING 122
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0000269|PubMed:12504901"
FT VARIANT 208
FT /note="K -> Q (in strain: NRRL Y-53)"
FT VARIANT 239
FT /note="A -> T (in strain: NRRL Y-53)"
FT VARIANT 262
FT /note="T -> S (in strain: NRRL Y-53)"
FT VARIANT 280..281
FT /note="LS -> IF (in strain: NRRL Y-53)"
FT MUTAGEN 109
FT /note="H->A: Stabilizes ubiquitin pathway substrates; when
FT associated wirh Ala-111."
FT /evidence="ECO:0000269|PubMed:12183636"
FT MUTAGEN 111
FT /note="H->A: Stabilizes ubiquitin pathway substrates; when
FT associated wirh Ala-109."
FT /evidence="ECO:0000269|PubMed:12183636"
FT STRAND 26..30
FT /evidence="ECO:0007829|PDB:5W83"
FT HELIX 31..44
FT /evidence="ECO:0007829|PDB:5W83"
FT STRAND 50..59
FT /evidence="ECO:0007829|PDB:5W83"
FT STRAND 62..70
FT /evidence="ECO:0007829|PDB:5W83"
FT STRAND 72..76
FT /evidence="ECO:0007829|PDB:5U4P"
FT HELIX 80..82
FT /evidence="ECO:0007829|PDB:4O8Y"
FT HELIX 85..97
FT /evidence="ECO:0007829|PDB:5W83"
FT STRAND 103..110
FT /evidence="ECO:0007829|PDB:5W83"
FT TURN 112..114
FT /evidence="ECO:0007829|PDB:5W83"
FT HELIX 120..132
FT /evidence="ECO:0007829|PDB:5W83"
FT STRAND 137..142
FT /evidence="ECO:0007829|PDB:5W83"
FT HELIX 145..148
FT /evidence="ECO:0007829|PDB:5W83"
FT STRAND 152..158
FT /evidence="ECO:0007829|PDB:5W83"
FT HELIX 162..166
FT /evidence="ECO:0007829|PDB:4OCM"
FT HELIX 182..194
FT /evidence="ECO:0007829|PDB:4OCM"
FT STRAND 196..204
FT /evidence="ECO:0007829|PDB:5W83"
FT HELIX 207..221
FT /evidence="ECO:0007829|PDB:5W83"
FT HELIX 230..260
FT /evidence="ECO:0007829|PDB:3JCK"
FT HELIX 263..270
FT /evidence="ECO:0007829|PDB:3JCK"
FT HELIX 276..305
FT /evidence="ECO:0007829|PDB:3JCK"
SQ SEQUENCE 306 AA; 34398 MW; 9DDE8BD74890894D CRC64;
MERLQRLMMN SKVGSADTGR DDTKETVYIS SIALLKMLKH GRAGVPMEVM GLMLGEFVDD
YTVNVVDVFA MPQSGTGVSV EAVDDVFQAK MMDMLKQTGR DQMVVGWYHS HPGFGCWLSS
VDVNTQKSFE QLNSRAVAVV VDPIQSVKGK VVIDAFRLID TGALINNLEP RQTTSNTGLL
NKANIQALIH GLNRHYYSLN IDYHKTAKET KMLMNLHKEQ WQSGLKMYDY EEKEESNLAA
TKSMVKIAEQ YSKRIEEEKE LTEEELKTRY VGRQDPKKHL SETADETLEN NIVSVLTAGV
NSVAIK
