DEAD_ECOLI
ID DEAD_ECOLI Reviewed; 629 AA.
AC P0A9P6; P23304; Q2M948; Q8FD90;
DT 19-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=ATP-dependent RNA helicase DeaD {ECO:0000255|HAMAP-Rule:MF_00964};
DE EC=3.6.4.13 {ECO:0000255|HAMAP-Rule:MF_00964};
DE AltName: Full=Cold-shock DEAD box protein A {ECO:0000255|HAMAP-Rule:MF_00964, ECO:0000303|PubMed:8552679};
DE AltName: Full=Translation factor W2;
GN Name=deaD {ECO:0000255|HAMAP-Rule:MF_00964, ECO:0000303|PubMed:15554978};
GN Synonyms=csdA {ECO:0000255|HAMAP-Rule:MF_00964,
GN ECO:0000303|PubMed:8552679}, mssB, rhlD; OrderedLocusNames=b3162, JW5531;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], SUPPRESSION OF RPSB MUTATION, AND GENE
RP NAME.
RX PubMed=2045359; DOI=10.1128/jb.173.11.3291-3302.1991;
RA Toone W.M., Rudd K.E., Friesen J.D.;
RT "deaD, a new Escherichia coli gene encoding a presumed ATP-dependent RNA
RT helicase, can suppress a mutation in rpsB, the gene encoding ribosomal
RT protein S2.";
RL J. Bacteriol. 173:3291-3302(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP PROTEIN SEQUENCE OF 2-21, FUNCTION IN HELIX-DESTABILIZING, INTERACTION WITH
RP RIBOSOME, SUBCELLULAR LOCATION, INDUCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=8552679; DOI=10.1073/pnas.93.1.76;
RA Jones P.G., Mitta M., Kim Y., Jiang W., Inouye M.;
RT "Cold shock induces a major ribosomal-associated protein that unwinds
RT double-stranded RNA in Escherichia coli.";
RL Proc. Natl. Acad. Sci. U.S.A. 93:76-80(1996).
RN [5]
RP PROTEIN SEQUENCE OF 2-16, AND FUNCTION AS A TRANSLATION FACTOR.
RX PubMed=10216955; DOI=10.1016/s1357-2725(98)00142-3;
RA Lu J., Aoki H., Ganoza M.C.;
RT "Molecular characterization of a prokaryotic translation factor homologous
RT to the eukaryotic initiation factor eIF4A.";
RL Int. J. Biochem. Cell Biol. 31:215-229(1999).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 519-629.
RC STRAIN=K12 / JM101 / ATCC 33876 / DSM 3948 / NCIMB 11926;
RX PubMed=8056751; DOI=10.1093/oxfordjournals.jbchem.a124352;
RA Peng H.L., Hsieh M.J., Zao C.L., Chang H.-Y.;
RT "Nucleotide sequence and expression in Escherichia coli of the Klebsiella
RT pneumoniae deaD gene.";
RL J. Biochem. 115:409-414(1994).
RN [7]
RP SUPPRESSION OF PYRH MUTATION.
RX PubMed=8190075; DOI=10.1007/bf00283870;
RA Yamanaka K., Ogura T., Koonin E.V., Niki H., Hiraga S.;
RT "Multicopy suppressors, mssA and mssB, of an smbA mutation of Escherichia
RT coli.";
RL Mol. Gen. Genet. 243:9-16(1994).
RN [8]
RP INDUCTION BY COLD-SHOCK.
RC STRAIN=CSH142;
RX PubMed=8898389; DOI=10.1111/j.1365-2958.1996.tb02582.x;
RA Jones P.G., Inouye M.;
RT "RbfA, a 30S ribosomal binding factor, is a cold-shock protein whose
RT absence triggers the cold-shock response.";
RL Mol. Microbiol. 21:1207-1218(1996).
RN [9]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=15196029; DOI=10.1021/bi049852s;
RA Bizebard T., Ferlenghi I., Iost I., Dreyfus M.;
RT "Studies on three E. coli DEAD-box helicases point to an unwinding
RT mechanism different from that of model DNA helicases.";
RL Biochemistry 43:7857-7866(2004).
RN [10]
RP FUNCTION IN MRNA DECAY, AND INTERACTION WITH RNASE E.
RC STRAIN=CF881;
RX PubMed=15554978; DOI=10.1111/j.1365-2958.2004.04360.x;
RA Prud'homme-Genereux A., Beran R.K., Iost I., Ramey C.S., Mackie G.A.,
RA Simons R.W.;
RT "Physical and functional interactions among RNase E, polynucleotide
RT phosphorylase and the cold-shock protein, CsdA: evidence for a 'cold shock
RT degradosome'.";
RL Mol. Microbiol. 54:1409-1421(2004).
RN [11]
RP FUNCTION IN 50S RIBOSOME BIOGENESIS, INTERACTION WITH 50S SUBUNIT, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=15148362; DOI=10.1093/nar/gkh603;
RA Charollais J., Dreyfus M., Iost I.;
RT "CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the
RT biogenesis of 50S ribosomal subunit.";
RL Nucleic Acids Res. 32:2751-2759(2004).
RN [12]
RP FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF GLU-157.
RX PubMed=17259309; DOI=10.1128/jb.01509-06;
RA Turner A.-M.W., Love C.F., Alexander R.W., Jones P.G.;
RT "Mutational analysis of the Escherichia coli DEAD box protein CsdA.";
RL J. Bacteriol. 189:2769-2776(2007).
RN [13]
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=25777676; DOI=10.1128/jb.00023-15;
RA Choudhury P., Flower A.M.;
RT "Efficient assembly of ribosomes is inhibited by deletion of bipA in
RT Escherichia coli.";
RL J. Bacteriol. 197:1819-1827(2015).
CC -!- FUNCTION: DEAD-box RNA helicase involved in various cellular processes
CC at low temperature, including ribosome biogenesis, mRNA degradation and
CC translation initiation. Exhibits RNA-stimulated ATP hydrolysis and RNA
CC unwinding activity at low temperature. Involved in 50S ribosomal
CC subunit assembly, acting after SrmB, and could also play a role in the
CC biogenesis of the 30S ribosomal subunit. In addition, is involved in
CC mRNA decay, via formation of a cold-shock degradosome with RNase E.
CC Also stimulates translation of some mRNAs, probably at the level of
CC initiation. {ECO:0000255|HAMAP-Rule:MF_00964,
CC ECO:0000269|PubMed:10216955, ECO:0000269|PubMed:15148362,
CC ECO:0000269|PubMed:15196029, ECO:0000269|PubMed:15554978,
CC ECO:0000269|PubMed:17259309, ECO:0000269|PubMed:8552679}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00964,
CC ECO:0000269|PubMed:15196029, ECO:0000269|PubMed:17259309};
CC -!- SUBUNIT: Interacts with the 50S ribosomal subunit upon shifting to 15
CC degrees Celsius. Also found associated with the RNA degradosome at 15
CC degrees Celsius; binds RNase E (rne). {ECO:0000269|PubMed:15148362,
CC ECO:0000269|PubMed:15554978, ECO:0000269|PubMed:8552679}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00964,
CC ECO:0000269|PubMed:8552679}.
CC -!- INDUCTION: In response to low temperature (PubMed:8552679). Induced by
CC cold shock (42 to 15 degrees Celsius) (at protein level)
CC (PubMed:8898389). {ECO:0000269|PubMed:8552679,
CC ECO:0000269|PubMed:8898389}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene grow very poorly at 15-20
CC degrees Celsius, and accumulate an abnormal large ribosomal subunit and
CC precursor-23S rRNA (PubMed:15148362, PubMed:8552679, PubMed:25777676).
CC A double bipA-deaD deletion has a more severe growth and ribosome
CC phenotype than either single deletion, but the same level of pre-23S
CC rRNA as the single deaD deletion (PubMed:25777676).
CC {ECO:0000269|PubMed:15148362, ECO:0000269|PubMed:25777676,
CC ECO:0000269|PubMed:8552679}.
CC -!- MISCELLANEOUS: When overexpressed suppresses cold-sensitive mutants of
CC rpsB (ribosomal protein S2) (PubMed:2045359) and pyrH/smbA2 (uridylate
CC kinase) (PubMed:8190075). {ECO:0000305|PubMed:2045359,
CC ECO:0000305|PubMed:8190075}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DeaD/CsdA
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_00964}.
CC -!- CAUTION: It is unclear whether it requires ATP: according to
CC PubMed:8552679 and PubMed:10216955, it does not require ATP, while
CC according to PubMed:15196029, PubMed:15554978 and PubMed:17259309, it
CC requires ATP. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA23674.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAA23674.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=AAA57965.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; M63288; AAA23674.1; ALT_SEQ; Genomic_DNA.
DR EMBL; U18997; AAA57965.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC76196.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE77208.1; -; Genomic_DNA.
DR EMBL; U03750; AAA03626.1; -; Genomic_DNA.
DR PIR; F65106; F65106.
DR RefSeq; NP_417631.2; NC_000913.3.
DR RefSeq; WP_001295553.1; NZ_STEB01000012.1.
DR PDB; 5B88; NMR; -; A=482-564.
DR PDB; 5GI4; X-ray; 2.24 A; A/B=218-445.
DR PDB; 5GJU; X-ray; 1.60 A; A=6-210.
DR PDBsum; 5B88; -.
DR PDBsum; 5GI4; -.
DR PDBsum; 5GJU; -.
DR AlphaFoldDB; P0A9P6; -.
DR SMR; P0A9P6; -.
DR BioGRID; 4262429; 170.
DR BioGRID; 851987; 1.
DR DIP; DIP-35752N; -.
DR IntAct; P0A9P6; 86.
DR STRING; 511145.b3162; -.
DR SWISS-2DPAGE; P0A9P6; -.
DR jPOST; P0A9P6; -.
DR PaxDb; P0A9P6; -.
DR PRIDE; P0A9P6; -.
DR EnsemblBacteria; AAC76196; AAC76196; b3162.
DR EnsemblBacteria; BAE77208; BAE77208; BAE77208.
DR GeneID; 60901957; -.
DR GeneID; 947674; -.
DR KEGG; ecj:JW5531; -.
DR KEGG; eco:b3162; -.
DR PATRIC; fig|1411691.4.peg.3568; -.
DR EchoBASE; EB0211; -.
DR eggNOG; COG0513; Bacteria.
DR HOGENOM; CLU_003041_21_1_6; -.
DR InParanoid; P0A9P6; -.
DR OMA; LPQGMPK; -.
DR PhylomeDB; P0A9P6; -.
DR BioCyc; EcoCyc:EG10215-MON; -.
DR BioCyc; MetaCyc:EG10215-MON; -.
DR BRENDA; 3.6.4.13; 2026.
DR PRO; PR:P0A9P6; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; IDA:EcoCyc.
DR GO; GO:0033592; F:RNA strand annealing activity; IDA:EcoCyc.
DR GO; GO:0070417; P:cellular response to cold; IMP:EcoCyc.
DR GO; GO:0048255; P:mRNA stabilization; IMP:CACAO.
DR GO; GO:0045727; P:positive regulation of translation; IMP:EcoCyc.
DR GO; GO:0009314; P:response to radiation; IMP:EcoCyc.
DR GO; GO:0000027; P:ribosomal large subunit assembly; IMP:EcoCyc.
DR GO; GO:0006401; P:RNA catabolic process; IEA:UniProtKB-UniRule.
DR CDD; cd12499; RRM_EcCsdA_like; 1.
DR Gene3D; 3.30.70.330; -; 1.
DR Gene3D; 3.40.50.300; -; 2.
DR HAMAP; MF_00964; DEAD_helicase_DeaD; 1.
DR InterPro; IPR021046; Cold-shock_DEAD_Abox_C.
DR InterPro; IPR034415; CsdA_RRM.
DR InterPro; IPR005580; DbpA/CsdA_RNA-bd_dom.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR028618; DEAD_helicase_DeaD.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR000629; RNA-helicase_DEAD-box_CS.
DR InterPro; IPR014014; RNA_helicase_DEAD_Q_motif.
DR Pfam; PF03880; DbpA; 1.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF12343; DeaD_C; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS00039; DEAD_ATP_HELICASE; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS51195; Q_MOTIF; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cytoplasm; Direct protein sequencing; Helicase;
KW Hydrolase; Nucleotide-binding; Reference proteome; RNA-binding;
KW Stress response.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:10216955,
FT ECO:0000269|PubMed:8552679"
FT CHAIN 2..629
FT /note="ATP-dependent RNA helicase DeaD"
FT /id="PRO_0000055101"
FT DOMAIN 37..208
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00964"
FT DOMAIN 232..379
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00964"
FT REGION 438..481
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 560..629
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 6..34
FT /note="Q motif"
FT MOTIF 156..159
FT /note="DEAD box"
FT COMPBIAS 446..481
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 575..629
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 50..57
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00964"
FT MUTAGEN 157
FT /note="E->Q: Abolishes ATPase activity, drastically reduces
FT helicase activity. In vivo acts as a dominant negative
FT mutation in the presence of the wild-type protein at low
FT temperature."
FT /evidence="ECO:0000269|PubMed:17259309"
FT CONFLICT 444
FT /note="A -> G (in Ref. 1; AAA23674)"
FT /evidence="ECO:0000305"
FT HELIX 9..11
FT /evidence="ECO:0007829|PDB:5GJU"
FT HELIX 15..24
FT /evidence="ECO:0007829|PDB:5GJU"
FT HELIX 31..41
FT /evidence="ECO:0007829|PDB:5GJU"
FT STRAND 46..48
FT /evidence="ECO:0007829|PDB:5GJU"
FT HELIX 56..66
FT /evidence="ECO:0007829|PDB:5GJU"
FT STRAND 77..80
FT /evidence="ECO:0007829|PDB:5GJU"
FT HELIX 84..97
FT /evidence="ECO:0007829|PDB:5GJU"
FT TURN 98..100
FT /evidence="ECO:0007829|PDB:5GJU"
FT STRAND 106..109
FT /evidence="ECO:0007829|PDB:5GJU"
FT HELIX 118..123
FT /evidence="ECO:0007829|PDB:5GJU"
FT STRAND 127..131
FT /evidence="ECO:0007829|PDB:5GJU"
FT HELIX 133..142
FT /evidence="ECO:0007829|PDB:5GJU"
FT STRAND 143..145
FT /evidence="ECO:0007829|PDB:5GJU"
FT STRAND 152..157
FT /evidence="ECO:0007829|PDB:5GJU"
FT HELIX 158..163
FT /evidence="ECO:0007829|PDB:5GJU"
FT HELIX 167..175
FT /evidence="ECO:0007829|PDB:5GJU"
FT STRAND 182..186
FT /evidence="ECO:0007829|PDB:5GJU"
FT HELIX 192..201
FT /evidence="ECO:0007829|PDB:5GJU"
FT STRAND 206..208
FT /evidence="ECO:0007829|PDB:5GJU"
FT STRAND 221..226
FT /evidence="ECO:0007829|PDB:5GI4"
FT HELIX 232..242
FT /evidence="ECO:0007829|PDB:5GI4"
FT STRAND 246..251
FT /evidence="ECO:0007829|PDB:5GI4"
FT HELIX 255..266
FT /evidence="ECO:0007829|PDB:5GI4"
FT TURN 267..269
FT /evidence="ECO:0007829|PDB:5GI4"
FT STRAND 272..275
FT /evidence="ECO:0007829|PDB:5GI4"
FT HELIX 282..292
FT /evidence="ECO:0007829|PDB:5GI4"
FT STRAND 298..301
FT /evidence="ECO:0007829|PDB:5GI4"
FT HELIX 304..306
FT /evidence="ECO:0007829|PDB:5GI4"
FT STRAND 314..321
FT /evidence="ECO:0007829|PDB:5GI4"
FT HELIX 326..333
FT /evidence="ECO:0007829|PDB:5GI4"
FT HELIX 338..340
FT /evidence="ECO:0007829|PDB:5GI4"
FT STRAND 344..349
FT /evidence="ECO:0007829|PDB:5GI4"
FT HELIX 351..353
FT /evidence="ECO:0007829|PDB:5GI4"
FT HELIX 354..363
FT /evidence="ECO:0007829|PDB:5GI4"
FT HELIX 376..395
FT /evidence="ECO:0007829|PDB:5GI4"
FT HELIX 400..406
FT /evidence="ECO:0007829|PDB:5GI4"
FT HELIX 407..409
FT /evidence="ECO:0007829|PDB:5GI4"
FT STRAND 414..416
FT /evidence="ECO:0007829|PDB:5GI4"
FT HELIX 421..432
FT /evidence="ECO:0007829|PDB:5GI4"
FT STRAND 489..492
FT /evidence="ECO:0007829|PDB:5B88"
FT TURN 495..498
FT /evidence="ECO:0007829|PDB:5B88"
FT HELIX 501..511
FT /evidence="ECO:0007829|PDB:5B88"
FT TURN 516..518
FT /evidence="ECO:0007829|PDB:5B88"
FT STRAND 529..531
FT /evidence="ECO:0007829|PDB:5B88"
FT HELIX 541..544
FT /evidence="ECO:0007829|PDB:5B88"
FT TURN 551..554
FT /evidence="ECO:0007829|PDB:5B88"
SQ SEQUENCE 629 AA; 70546 MW; 9DB692D41C38D17C CRC64;
MAEFETTFAD LGLKAPILEA LNDLGYEKPS PIQAECIPHL LNGRDVLGMA QTGSGKTAAF
SLPLLQNLDP ELKAPQILVL APTRELAVQV AEAMTDFSKH MRGVNVVALY GGQRYDVQLR
ALRQGPQIVV GTPGRLLDHL KRGTLDLSKL SGLVLDEADE MLRMGFIEDV ETIMAQIPEG
HQTALFSATM PEAIRRITRR FMKEPQEVRI QSSVTTRPDI SQSYWTVWGM RKNEALVRFL
EAEDFDAAII FVRTKNATLE VAEALERNGY NSAALNGDMN QALREQTLER LKDGRLDILI
ATDVAARGLD VERISLVVNY DIPMDSESYV HRIGRTGRAG RAGRALLFVE NRERRLLRNI
ERTMKLTIPE VELPNAELLG KRRLEKFAAK VQQQLESSDL DQYRALLSKI QPTAEGEELD
LETLAAALLK MAQGERTLIV PPDAPMRPKR EFRDRDDRGP RDRNDRGPRG DREDRPRRER
RDVGDMQLYR IEVGRDDGVE VRHIVGAIAN EGDISSRYIG NIKLFASHST IELPKGMPGE
VLQHFTRTRI LNKPMNMQLL GDAQPHTGGE RRGGGRGFGG ERREGGRNFS GERREGGRGD
GRRFSGERRE GRAPRRDDST GRRRFGGDA