DNK_DROME
ID DNK_DROME Reviewed; 250 AA.
AC Q9XZT6;
DT 02-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 156.
DE RecName: Full=Deoxynucleoside kinase;
DE EC=2.7.1.145 {ECO:0000269|PubMed:10446143, ECO:0000269|PubMed:10692477, ECO:0000269|PubMed:16008571, ECO:0000269|PubMed:9461577};
DE AltName: Full=Deoxyribonucleoside kinase;
DE Short=Dm-dNK;
DE AltName: Full=Multispecific deoxynucleoside kinase;
GN Name=dnk; ORFNames=CG5452;
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC Drosophilidae; Drosophila; Sophophora.
OX NCBI_TaxID=7227;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND CHARACTERIZATION.
RX PubMed=10446143; DOI=10.1074/jbc.274.34.23814;
RA Johansson M., Van Rompay A.R., Degreve B., Balzarini J., Karlsson A.;
RT "Cloning and characterization of the multisubstrate deoxyribonucleoside
RT kinase of Drosophila melanogaster.";
RL J. Biol. Chem. 274:23814-23819(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND CHARACTERIZATION.
RC STRAIN=Oregon-R;
RX PubMed=10692477; DOI=10.1074/jbc.275.9.6673;
RA Munch-Petersen B., Knecht W., Lenz C., Sondergaard L., Piskur J.;
RT "Functional expression of a multisubstrate deoxyribonucleoside kinase from
RT Drosophila melanogaster and its C-terminal deletion mutants.";
RL J. Biol. Chem. 275:6673-6679(2000).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley;
RX PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C.,
RA Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C.,
RA Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A.,
RA An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A.,
RA Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V.,
RA Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J.,
RA Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E.,
RA Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B.,
RA Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I.,
RA Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C.,
RA Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S.,
RA Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M.,
RA Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
RA Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D.,
RA Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F.,
RA Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D.,
RA Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A.,
RA Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C.,
RA McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C.,
RA Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L.,
RA Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R.,
RA Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V.,
RA Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F.,
RA Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
RA Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R.,
RA Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y.,
RA Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T.,
RA Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S.,
RA Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W.,
RA Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M.,
RA Venter J.C.;
RT "The genome sequence of Drosophila melanogaster.";
RL Science 287:2185-2195(2000).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=Berkeley;
RX PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
RA Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
RA Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
RA Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
RA Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
RA Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M.,
RA Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.;
RT "Annotation of the Drosophila melanogaster euchromatic genome: a systematic
RT review.";
RL Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
RN [5]
RP ENZYME ACTIVITY, AND SUBUNIT.
RX PubMed=9461577; DOI=10.1074/jbc.273.7.3926;
RA Munch-Petersen B., Piskur J., Sondergaard L.;
RT "Four deoxynucleoside kinase activities from Drosophila melanogaster are
RT contained within a single monomeric enzyme, a new multifunctional
RT deoxynucleoside kinase.";
RL J. Biol. Chem. 273:3926-3931(1998).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-241, AND IDENTIFICATION BY
RP MASS SPECTROMETRY.
RX PubMed=17372656; DOI=10.1039/b617545g;
RA Bodenmiller B., Mueller L.N., Pedrioli P.G.A., Pflieger D., Juenger M.A.,
RA Eng J.K., Aebersold R., Tao W.A.;
RT "An integrated chemical, mass spectrometric and computational strategy for
RT (quantitative) phosphoproteomics: application to Drosophila melanogaster
RT Kc167 cells.";
RL Mol. Biosyst. 3:275-286(2007).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-236 AND SER-243, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC TISSUE=Embryo;
RX PubMed=18327897; DOI=10.1021/pr700696a;
RA Zhai B., Villen J., Beausoleil S.A., Mintseris J., Gygi S.P.;
RT "Phosphoproteome analysis of Drosophila melanogaster embryos.";
RL J. Proteome Res. 7:1675-1682(2008).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 1-230 IN COMPLEXES WITH
RP DEOXYTHIMIDINE AND DEOXY-TTP.
RX PubMed=12741827; DOI=10.1021/bi0340043;
RA Mikkelsen N.E., Johansson K., Karlsson A., Knecht W., Andersen G.,
RA Piskur J., Munch-Petersen B., Eklund H.;
RT "Structural basis for feedback inhibition of the deoxyribonucleoside
RT salvage pathway: studies of the Drosophila deoxyribonucleoside kinase.";
RL Biochemistry 42:5706-5712(2003).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 1-230 OF MUTANT ASP-45/ASP-64 IN
RP COMPLEXES WITH THYMIDINE AND TTP, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS
RP OF ASN-45 AND ASN-64, AND ACTIVITY REGULATION.
RX PubMed=16008571; DOI=10.1111/j.1742-4658.2005.04803.x;
RA Welin M., Skovgaard T., Knecht W., Zhu C., Berenstein D.,
RA Munch-Petersen B., Piskur J., Eklund H.;
RT "Structural basis for the changed substrate specificity of Drosophila
RT melanogaster deoxyribonucleoside kinase mutant N64D.";
RL FEBS J. 272:3733-3742(2005).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEXES WITH DEOXY-CTP;
RP DEOXY-GTP; DEOXY-TTP; FLOXURIDINE; AZIDO-DIDEOXYTHYMIDINE; DIDEOXYCYTIDINE
RP AND BRIVUDINE.
RX PubMed=18384378; DOI=10.1111/j.1742-4658.2008.06369.x;
RA Mikkelsen N.E., Munch-Petersen B., Eklund H.;
RT "Structural studies of nucleoside analog and feedback inhibitor binding to
RT Drosophila melanogaster multisubstrate deoxyribonucleoside kinase.";
RL FEBS J. 275:2151-2160(2008).
CC -!- FUNCTION: Deoxyribonucleoside kinase that has a broad specificity
CC phosphorylating thymidine, 2'-deoxyriboadenosine, 2'-deoxyribocytidine
CC and 2'-deoxyriboguanosine. Specificity is higher for pyrimidine
CC nucleosides. Several anti-viral and anti-cancer nucleoside analogs are
CC also efficiently phosphorylated. {ECO:0000269|PubMed:10446143,
CC ECO:0000269|PubMed:10692477, ECO:0000269|PubMed:16008571}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside + ATP = a 2'-deoxyribonucleoside 5'-
CC phosphate + ADP + H(+); Xref=Rhea:RHEA:12140, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:18274, ChEBI:CHEBI:30616, ChEBI:CHEBI:65317,
CC ChEBI:CHEBI:456216; EC=2.7.1.145;
CC Evidence={ECO:0000269|PubMed:10446143, ECO:0000269|PubMed:10692477,
CC ECO:0000269|PubMed:16008571, ECO:0000269|PubMed:9461577};
CC -!- ACTIVITY REGULATION: Subject to feedback inhibition by dTTP.
CC {ECO:0000269|PubMed:16008571}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.9 uM for thymidine {ECO:0000269|PubMed:10446143,
CC ECO:0000269|PubMed:10692477};
CC KM=1 uM for deoxycytidine {ECO:0000269|PubMed:10446143,
CC ECO:0000269|PubMed:10692477};
CC KM=109 uM for deoxyadenosine {ECO:0000269|PubMed:10446143,
CC ECO:0000269|PubMed:10692477};
CC KM=654 uM for deoxyguanosine {ECO:0000269|PubMed:10446143,
CC ECO:0000269|PubMed:10692477};
CC Vmax=29.4 mmol/min/mg enzyme with thymidine as substrate
CC {ECO:0000269|PubMed:10446143, ECO:0000269|PubMed:10692477};
CC Vmax=28.7 mmol/min/mg enzyme with deoxycytidine as substrate
CC {ECO:0000269|PubMed:10446143, ECO:0000269|PubMed:10692477};
CC Vmax=35.5 mmol/min/mg enzyme with deoxyadenosine as substrate
CC {ECO:0000269|PubMed:10446143, ECO:0000269|PubMed:10692477};
CC Vmax=37.7 mmol/min/mg enzyme with deoxyguanosine as substrate
CC {ECO:0000269|PubMed:10446143, ECO:0000269|PubMed:10692477};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:9461577}.
CC -!- SIMILARITY: Belongs to the DCK/DGK family. {ECO:0000305}.
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DR EMBL; AF045610; AAD47355.2; -; mRNA.
DR EMBL; AF185268; AAD56545.1; -; Genomic_DNA.
DR EMBL; Y18048; CAB41881.1; -; mRNA.
DR EMBL; AE014297; AAF55615.1; -; Genomic_DNA.
DR RefSeq; NP_001262722.1; NM_001275793.1.
DR RefSeq; NP_524399.1; NM_079675.3.
DR PDB; 1J90; X-ray; 2.56 A; A/B=1-230.
DR PDB; 1OE0; X-ray; 2.40 A; A/B/C/D=1-230.
DR PDB; 1OT3; X-ray; 2.50 A; A/B/C/D/E/F/G/H=1-250.
DR PDB; 1ZM7; X-ray; 2.20 A; A/B/C/D=1-230.
DR PDB; 1ZMX; X-ray; 3.10 A; A/B/C/D/E/F/G/H=1-230.
DR PDB; 2JCS; X-ray; 2.50 A; A/B=1-230.
DR PDB; 2JJ8; X-ray; 2.80 A; A/B/C/D=1-230.
DR PDB; 2VP0; X-ray; 2.20 A; A/B=1-250.
DR PDB; 2VP2; X-ray; 2.50 A; A/B=1-230.
DR PDB; 2VP4; X-ray; 2.20 A; A/B/C/D=1-230.
DR PDB; 2VP5; X-ray; 2.30 A; A/B=1-230.
DR PDB; 2VP6; X-ray; 3.00 A; A/B/C/D/E/F/G/H=1-230.
DR PDB; 2VP9; X-ray; 2.90 A; A/B/C/D/E/F/G/H=1-230.
DR PDB; 2VPP; X-ray; 2.20 A; A/B=1-230.
DR PDB; 2VQS; X-ray; 2.90 A; A/B/C/D=1-230.
DR PDB; 6YBH; X-ray; 2.40 A; A/B/C/D/E/F=13-235.
DR PDBsum; 1J90; -.
DR PDBsum; 1OE0; -.
DR PDBsum; 1OT3; -.
DR PDBsum; 1ZM7; -.
DR PDBsum; 1ZMX; -.
DR PDBsum; 2JCS; -.
DR PDBsum; 2JJ8; -.
DR PDBsum; 2VP0; -.
DR PDBsum; 2VP2; -.
DR PDBsum; 2VP4; -.
DR PDBsum; 2VP5; -.
DR PDBsum; 2VP6; -.
DR PDBsum; 2VP9; -.
DR PDBsum; 2VPP; -.
DR PDBsum; 2VQS; -.
DR PDBsum; 6YBH; -.
DR AlphaFoldDB; Q9XZT6; -.
DR SMR; Q9XZT6; -.
DR BioGRID; 67276; 9.
DR DIP; DIP-23491N; -.
DR IntAct; Q9XZT6; 3.
DR STRING; 7227.FBpp0302815; -.
DR BindingDB; Q9XZT6; -.
DR ChEMBL; CHEMBL4760; -.
DR DrugCentral; Q9XZT6; -.
DR iPTMnet; Q9XZT6; -.
DR PaxDb; Q9XZT6; -.
DR PRIDE; Q9XZT6; -.
DR DNASU; 42273; -.
DR EnsemblMetazoa; FBtr0083707; FBpp0083121; FBgn0022338.
DR EnsemblMetazoa; FBtr0321263; FBpp0302815; FBgn0022338.
DR GeneID; 42273; -.
DR KEGG; dme:Dmel_CG5452; -.
DR CTD; 42273; -.
DR FlyBase; FBgn0022338; dnk.
DR VEuPathDB; VectorBase:FBgn0022338; -.
DR eggNOG; KOG4235; Eukaryota.
DR GeneTree; ENSGT00940000158005; -.
DR HOGENOM; CLU_030466_1_0_1; -.
DR InParanoid; Q9XZT6; -.
DR OMA; KYRDEIC; -.
DR OrthoDB; 1505356at2759; -.
DR PhylomeDB; Q9XZT6; -.
DR BioCyc; MetaCyc:MON-17889; -.
DR BRENDA; 2.7.1.145; 1994.
DR Reactome; R-DME-73614; Pyrimidine salvage.
DR SABIO-RK; Q9XZT6; -.
DR BioGRID-ORCS; 42273; 0 hits in 3 CRISPR screens.
DR EvolutionaryTrace; Q9XZT6; -.
DR GenomeRNAi; 42273; -.
DR PRO; PR:Q9XZT6; -.
DR Proteomes; UP000000803; Chromosome 3R.
DR Bgee; FBgn0022338; Expressed in cleaving embryo and 50 other tissues.
DR ExpressionAtlas; Q9XZT6; baseline and differential.
DR Genevisible; Q9XZT6; DM.
DR GO; GO:0005737; C:cytoplasm; IDA:FlyBase.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0043771; F:cytidine kinase activity; IDA:FlyBase.
DR GO; GO:0004136; F:deoxyadenosine kinase activity; IDA:FlyBase.
DR GO; GO:0004137; F:deoxycytidine kinase activity; IDA:FlyBase.
DR GO; GO:0004138; F:deoxyguanosine kinase activity; IDA:FlyBase.
DR GO; GO:0019136; F:deoxynucleoside kinase activity; IDA:UniProtKB.
DR GO; GO:0016301; F:kinase activity; IDA:FlyBase.
DR GO; GO:0004797; F:thymidine kinase activity; IDA:FlyBase.
DR GO; GO:0004849; F:uridine kinase activity; IDA:FlyBase.
DR GO; GO:0071897; P:DNA biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0006165; P:nucleoside diphosphate phosphorylation; IDA:UniProtKB.
DR GO; GO:1901293; P:nucleoside phosphate biosynthetic process; IDA:FlyBase.
DR GO; GO:0046939; P:nucleotide phosphorylation; IDA:FlyBase.
DR GO; GO:0016310; P:phosphorylation; IDA:FlyBase.
DR CDD; cd01673; dNK; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR002624; DCK/DGK.
DR InterPro; IPR031314; DNK_dom.
DR InterPro; IPR027417; P-loop_NTPase.
DR Pfam; PF01712; dNK; 1.
DR PIRSF; PIRSF000705; DNK; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; DNA synthesis; Kinase; Nucleotide-binding;
KW Phosphoprotein; Reference proteome; Transferase.
FT CHAIN 1..250
FT /note="Deoxynucleoside kinase"
FT /id="PRO_0000175097"
FT ACT_SITE 104
FT /note="Proton acceptor"
FT /evidence="ECO:0000255"
FT BINDING 27..35
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 52
FT /ligand="substrate"
FT BINDING 70
FT /ligand="substrate"
FT BINDING 81
FT /ligand="substrate"
FT BINDING 105
FT /ligand="substrate"
FT BINDING 172
FT /ligand="substrate"
FT MOD_RES 236
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18327897"
FT MOD_RES 241
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:17372656"
FT MOD_RES 243
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18327897"
FT MUTAGEN 45
FT /note="N->D: Reduces enzyme activity towards dA, dG, dT and
FT dC about 5-fold."
FT /evidence="ECO:0000269|PubMed:16008571"
FT MUTAGEN 64
FT /note="N->D: Reduces enzyme activity towards dT and dC
FT about 500-fold. Reduces enzyme activity towards dG about
FT 3900-fold. Reduces enzyme activity towards dA about 900-
FT fold."
FT /evidence="ECO:0000269|PubMed:16008571"
FT TURN 15..17
FT /evidence="ECO:0007829|PDB:1ZM7"
FT STRAND 21..28
FT /evidence="ECO:0007829|PDB:1ZM7"
FT HELIX 33..38
FT /evidence="ECO:0007829|PDB:1ZM7"
FT HELIX 39..43
FT /evidence="ECO:0007829|PDB:1ZM7"
FT TURN 44..46
FT /evidence="ECO:0007829|PDB:1ZM7"
FT STRAND 47..50
FT /evidence="ECO:0007829|PDB:1ZM7"
FT HELIX 54..57
FT /evidence="ECO:0007829|PDB:1ZM7"
FT STRAND 60..62
FT /evidence="ECO:0007829|PDB:2VP5"
FT HELIX 65..71
FT /evidence="ECO:0007829|PDB:1ZM7"
FT HELIX 73..93
FT /evidence="ECO:0007829|PDB:1ZM7"
FT STRAND 98..105
FT /evidence="ECO:0007829|PDB:1ZM7"
FT HELIX 107..112
FT /evidence="ECO:0007829|PDB:1ZM7"
FT HELIX 114..120
FT /evidence="ECO:0007829|PDB:1ZM7"
FT STRAND 122..124
FT /evidence="ECO:0007829|PDB:2VP4"
FT HELIX 126..142
FT /evidence="ECO:0007829|PDB:1ZM7"
FT STRAND 148..154
FT /evidence="ECO:0007829|PDB:1ZM7"
FT HELIX 157..167
FT /evidence="ECO:0007829|PDB:1ZM7"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:1ZM7"
FT HELIX 177..191
FT /evidence="ECO:0007829|PDB:1ZM7"
FT TURN 192..194
FT /evidence="ECO:0007829|PDB:1J90"
FT STRAND 200..206
FT /evidence="ECO:0007829|PDB:1ZM7"
FT TURN 212..217
FT /evidence="ECO:0007829|PDB:6YBH"
FT HELIX 224..226
FT /evidence="ECO:0007829|PDB:6YBH"
SQ SEQUENCE 250 AA; 29088 MW; 17C5DF197B8792DB CRC64;
MAEAASCARK GTKYAEGTQP FTVLIEGNIG SGKTTYLNHF EKYKNDICLL TEPVEKWRNV
NGVNLLELMY KDPKKWAMPF QSYVTLTMLQ SHTAPTNKKL KIMERSIFSA RYCFVENMRR
NGSLEQGMYN TLEEWYKFIE ESIHVQADLI IYLRTSPEVA YERIRQRARS EESCVPLKYL
QELHELHEDW LIHQRRPQSC KVLVLDADLN LENIGTEYQR SESSIFDAIS SNQQPSPVLV
SPSKRQRVAR
