PARE_STRPN
ID PARE_STRPN Reviewed; 647 AA.
AC Q59961; P77956;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 26-SEP-2001, sequence version 3.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=DNA topoisomerase 4 subunit B {ECO:0000255|HAMAP-Rule:MF_00939};
DE EC=5.6.2.2 {ECO:0000255|HAMAP-Rule:MF_00939, ECO:0000269|PubMed:17375187, ECO:0000269|PubMed:20596531};
DE AltName: Full=Topoisomerase IV subunit B {ECO:0000255|HAMAP-Rule:MF_00939};
GN Name=parE {ECO:0000255|HAMAP-Rule:MF_00939}; OrderedLocusNames=SP_0852;
OS Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=170187;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=7785;
RX PubMed=8763932; DOI=10.1128/jb.178.14.4060-4069.1996;
RA Pan X., Fisher M.;
RT "Cloning and characterization of the parC and parE genes of Streptococcus
RT pneumoniae encoding DNA topoisomerase IV: role in fluoroquinolone
RT resistance.";
RL J. Bacteriol. 178:4060-4069(1996).
RN [2]
RP SEQUENCE REVISION TO 329; 347 AND 351.
RA Pan X.;
RL Submitted (JAN-2000) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-334 / TIGR4;
RX PubMed=11463916; DOI=10.1126/science.1061217;
RA Tettelin H., Nelson K.E., Paulsen I.T., Eisen J.A., Read T.D.,
RA Peterson S.N., Heidelberg J.F., DeBoy R.T., Haft D.H., Dodson R.J.,
RA Durkin A.S., Gwinn M.L., Kolonay J.F., Nelson W.C., Peterson J.D.,
RA Umayam L.A., White O., Salzberg S.L., Lewis M.R., Radune D.,
RA Holtzapple E.K., Khouri H.M., Wolf A.M., Utterback T.R., Hansen C.L.,
RA McDonald L.A., Feldblyum T.V., Angiuoli S.V., Dickinson T., Hickey E.K.,
RA Holt I.E., Loftus B.J., Yang F., Smith H.O., Venter J.C., Dougherty B.A.,
RA Morrison D.A., Hollingshead S.K., Fraser C.M.;
RT "Complete genome sequence of a virulent isolate of Streptococcus
RT pneumoniae.";
RL Science 293:498-506(2001).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 93-647.
RC STRAIN=D39 / NCTC 7466 / Serotype 2;
RX PubMed=8891124; DOI=10.1128/aac.40.10.2252;
RA Munoz R., de la Campa A.G.;
RT "ParC subunit of DNA topoisomerase IV of Streptococcus pneumoniae is a
RT primary target of fluoroquinolones and cooperates with DNA gyrase A subunit
RT in forming resistance phenotype.";
RL Antimicrob. Agents Chemother. 40:2252-2257(1996).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
RX PubMed=17375187; DOI=10.1371/journal.pone.0000301;
RA Laponogov I., Veselkov D.A., Sohi M.K., Pan X.S., Achari A., Yang C.,
RA Ferrara J.D., Fisher L.M., Sanderson M.R.;
RT "Breakage-reunion domain of Streptococcus pneumoniae topoisomerase IV:
RT crystal structure of a gram-positive quinolone target.";
RL PLoS ONE 2:E301-E301(2007).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (4.0 ANGSTROMS) OF 404-647 IN COMPLEX WITH PARC AND
RP DNA, AND SUBUNIT.
RX PubMed=19448616; DOI=10.1038/nsmb.1604;
RA Laponogov I., Sohi M.K., Veselkov D.A., Pan X.S., Sawhney R.,
RA Thompson A.W., McAuley K.E., Fisher L.M., Sanderson M.R.;
RT "Structural insight into the quinolone-DNA cleavage complex of type IIA
RT topoisomerases.";
RL Nat. Struct. Mol. Biol. 16:667-669(2009).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF 404-647 IN COMPLEX WITH PARC;
RP MAGNESIUM; LEVOFLOXACIN AND DNA, CATALYTIC ACTIVITY, FUNCTION, ACTIVITY
RP REGULATION, COFACTOR, AND SUBUNIT.
RX PubMed=20596531; DOI=10.1371/journal.pone.0011338;
RA Laponogov I., Pan X.S., Veselkov D.A., McAuley K.E., Fisher L.M.,
RA Sanderson M.R.;
RT "Structural basis of gate-DNA breakage and resealing by type II
RT topoisomerases.";
RL PLoS ONE 5:E11338-E11338(2010).
CC -!- FUNCTION: Topoisomerase IV is essential for chromosome segregation. It
CC relaxes supercoiled DNA. Performs the decatenation events required
CC during the replication of a circular DNA molecule. {ECO:0000255|HAMAP-
CC Rule:MF_00939, ECO:0000269|PubMed:17375187,
CC ECO:0000269|PubMed:20596531}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-dependent breakage, passage and rejoining of double-
CC stranded DNA.; EC=5.6.2.2; Evidence={ECO:0000255|HAMAP-Rule:MF_00939,
CC ECO:0000269|PubMed:17375187, ECO:0000269|PubMed:20596531};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00939,
CC ECO:0000269|PubMed:20596531};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00939,
CC ECO:0000269|PubMed:20596531};
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00939,
CC ECO:0000269|PubMed:20596531};
CC Note=Binds two Mg(2+) per subunit. The magnesium ions form salt bridges
CC with both the protein and the DNA. Can also accept other divalent metal
CC cations, such as Mn(2+) or Ca(2+). {ECO:0000255|HAMAP-Rule:MF_00939,
CC ECO:0000269|PubMed:20596531};
CC -!- ACTIVITY REGULATION: Inhibited by quinolones, such as levofloxacin.
CC {ECO:0000269|PubMed:20596531}.
CC -!- SUBUNIT: Heterotetramer composed of ParC and ParE. {ECO:0000255|HAMAP-
CC Rule:MF_00939, ECO:0000269|PubMed:17375187,
CC ECO:0000269|PubMed:19448616, ECO:0000269|PubMed:20596531}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase family. ParE type 2
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_00939}.
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DR EMBL; Z67739; CAA91550.2; -; Genomic_DNA.
DR EMBL; AE005672; AAK74981.1; -; Genomic_DNA.
DR EMBL; X95717; CAA65022.1; -; Genomic_DNA.
DR PIR; D95098; D95098.
DR RefSeq; WP_000037283.1; NZ_AKVY01000001.1.
DR PDB; 3FOE; X-ray; 4.00 A; C/D=404-647.
DR PDB; 3FOF; X-ray; 4.00 A; C/D=404-647.
DR PDB; 3K9F; X-ray; 2.90 A; C/D=404-647.
DR PDB; 3KSA; X-ray; 3.30 A; C/D=404-647.
DR PDB; 3KSB; X-ray; 3.50 A; C/D=404-647.
DR PDB; 3LTN; X-ray; 3.10 A; C/D=404-647.
DR PDB; 3RAD; X-ray; 3.35 A; C/D=404-647.
DR PDB; 3RAE; X-ray; 2.90 A; C/D=404-647.
DR PDB; 3RAF; X-ray; 3.24 A; C/D=404-647.
DR PDB; 4I3H; X-ray; 3.70 A; A/B=1-647.
DR PDB; 4JUO; X-ray; 6.53 A; C=1-647.
DR PDB; 4KOE; X-ray; 3.02 A; C/D=404-647.
DR PDB; 4KPE; X-ray; 3.43 A; C/D=404-647.
DR PDB; 4KPF; X-ray; 3.24 A; C/D=404-647.
DR PDB; 4Z3O; X-ray; 3.44 A; A/B=404-643.
DR PDB; 4Z4Q; X-ray; 3.04 A; A/B=404-643.
DR PDB; 4Z53; X-ray; 3.26 A; A/B=404-643.
DR PDB; 5J5P; X-ray; 1.97 A; A/B=1-402.
DR PDB; 5J5Q; X-ray; 2.83 A; A/B/C/D=1-402.
DR PDBsum; 3FOE; -.
DR PDBsum; 3FOF; -.
DR PDBsum; 3K9F; -.
DR PDBsum; 3KSA; -.
DR PDBsum; 3KSB; -.
DR PDBsum; 3LTN; -.
DR PDBsum; 3RAD; -.
DR PDBsum; 3RAE; -.
DR PDBsum; 3RAF; -.
DR PDBsum; 4I3H; -.
DR PDBsum; 4JUO; -.
DR PDBsum; 4KOE; -.
DR PDBsum; 4KPE; -.
DR PDBsum; 4KPF; -.
DR PDBsum; 4Z3O; -.
DR PDBsum; 4Z4Q; -.
DR PDBsum; 4Z53; -.
DR PDBsum; 5J5P; -.
DR PDBsum; 5J5Q; -.
DR AlphaFoldDB; Q59961; -.
DR SMR; Q59961; -.
DR DIP; DIP-48520N; -.
DR IntAct; Q59961; 1.
DR STRING; 170187.SP_0852; -.
DR ChEMBL; CHEMBL2363033; -.
DR DrugBank; DB01044; Gatifloxacin.
DR DrugCentral; Q59961; -.
DR EnsemblBacteria; AAK74981; AAK74981; SP_0852.
DR KEGG; spn:SP_0852; -.
DR eggNOG; COG0187; Bacteria.
DR OMA; KIAYAWT; -.
DR PhylomeDB; Q59961; -.
DR BioCyc; SPNE170187:G1FZB-872-MON; -.
DR EvolutionaryTrace; Q59961; -.
DR PRO; PR:Q59961; -.
DR Proteomes; UP000000585; Chromosome.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003918; F:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0007059; P:chromosome segregation; IEA:UniProtKB-UniRule.
DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule.
DR Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.30.565.10; -; 1.
DR Gene3D; 3.40.50.670; -; 1.
DR HAMAP; MF_00939; ParE_type2; 1.
DR InterPro; IPR002288; DNA_gyrase_B_C.
DR InterPro; IPR003594; HATPase_C.
DR InterPro; IPR036890; HATPase_C_sf.
DR InterPro; IPR005740; ParE_type2.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR InterPro; IPR014721; Ribosomal_S5_D2-typ_fold_subgr.
DR InterPro; IPR001241; Topo_IIA.
DR InterPro; IPR013760; Topo_IIA-like_dom_sf.
DR InterPro; IPR013759; Topo_IIA_B_C.
DR InterPro; IPR013506; Topo_IIA_bsu_dom2.
DR InterPro; IPR018522; TopoIIA_CS.
DR InterPro; IPR006171; TOPRIM_domain.
DR Pfam; PF00204; DNA_gyraseB; 1.
DR Pfam; PF00986; DNA_gyraseB_C; 1.
DR Pfam; PF02518; HATPase_c; 1.
DR Pfam; PF01751; Toprim; 1.
DR SMART; SM00387; HATPase_c; 1.
DR SMART; SM00433; TOP2c; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55874; SSF55874; 1.
DR SUPFAM; SSF56719; SSF56719; 1.
DR TIGRFAMs; TIGR01058; parE_Gpos; 1.
DR PROSITE; PS00177; TOPOISOMERASE_II; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; DNA-binding; Isomerase; Magnesium;
KW Metal-binding; Nucleotide-binding; Topoisomerase.
FT CHAIN 1..647
FT /note="DNA topoisomerase 4 subunit B"
FT /id="PRO_0000145443"
FT DOMAIN 427..541
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00939"
FT REGION 391..421
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 391..411
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 11
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00939"
FT BINDING 51
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00939"
FT BINDING 78
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00939"
FT BINDING 118..124
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00939"
FT BINDING 344
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00939"
FT BINDING 433
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00939,
FT ECO:0000269|PubMed:20596531"
FT BINDING 506
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00939,
FT ECO:0000269|PubMed:20596531"
FT BINDING 506
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00939,
FT ECO:0000269|PubMed:20596531"
FT BINDING 508
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00939,
FT ECO:0000269|PubMed:20596531"
FT SITE 458
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00939"
FT SITE 461
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00939"
FT SITE 513
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00939"
FT SITE 629
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00939"
FT CONFLICT 166
FT /note="P -> L (in Ref. 4; CAA65022)"
FT /evidence="ECO:0000305"
FT CONFLICT 217
FT /note="N -> D (in Ref. 1 and 4)"
FT /evidence="ECO:0000305"
FT CONFLICT 460
FT /note="V -> I (in Ref. 1 and 4)"
FT /evidence="ECO:0000305"
FT CONFLICT 568
FT /note="R -> L (in Ref. 4; CAA65022)"
FT /evidence="ECO:0000305"
FT CONFLICT 644
FT /note="T -> A (in Ref. 1 and 4)"
FT /evidence="ECO:0000305"
FT HELIX 13..15
FT /evidence="ECO:0007829|PDB:5J5P"
FT HELIX 21..27
FT /evidence="ECO:0007829|PDB:5J5P"
FT HELIX 29..33
FT /evidence="ECO:0007829|PDB:5J5P"
FT HELIX 38..57
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 62..68
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 74..78
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 86..88
FT /evidence="ECO:0007829|PDB:5J5Q"
FT STRAND 91..93
FT /evidence="ECO:0007829|PDB:5J5P"
FT HELIX 94..100
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 104..106
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 108..112
FT /evidence="ECO:0007829|PDB:5J5P"
FT HELIX 123..129
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 131..140
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 143..150
FT /evidence="ECO:0007829|PDB:5J5P"
FT TURN 151..153
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 154..157
FT /evidence="ECO:0007829|PDB:5J5Q"
FT STRAND 160..164
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 171..178
FT /evidence="ECO:0007829|PDB:5J5P"
FT TURN 180..182
FT /evidence="ECO:0007829|PDB:5J5P"
FT HELIX 190..202
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 208..213
FT /evidence="ECO:0007829|PDB:5J5P"
FT TURN 214..217
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 218..222
FT /evidence="ECO:0007829|PDB:5J5P"
FT HELIX 227..235
FT /evidence="ECO:0007829|PDB:5J5P"
FT TURN 236..238
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 241..243
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 246..252
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 255..267
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 270..275
FT /evidence="ECO:0007829|PDB:5J5P"
FT HELIX 285..304
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 310..312
FT /evidence="ECO:0007829|PDB:5J5Q"
FT HELIX 317..321
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 324..331
FT /evidence="ECO:0007829|PDB:5J5P"
FT HELIX 334..336
FT /evidence="ECO:0007829|PDB:5J5P"
FT TURN 341..344
FT /evidence="ECO:0007829|PDB:5J5P"
FT STRAND 345..347
FT /evidence="ECO:0007829|PDB:5J5Q"
FT HELIX 352..370
FT /evidence="ECO:0007829|PDB:5J5P"
FT HELIX 372..399
FT /evidence="ECO:0007829|PDB:5J5P"
FT TURN 424..426
FT /evidence="ECO:0007829|PDB:3RAE"
FT STRAND 428..433
FT /evidence="ECO:0007829|PDB:3K9F"
FT HELIX 435..443
FT /evidence="ECO:0007829|PDB:3K9F"
FT TURN 447..449
FT /evidence="ECO:0007829|PDB:3K9F"
FT STRAND 450..455
FT /evidence="ECO:0007829|PDB:3K9F"
FT TURN 462..464
FT /evidence="ECO:0007829|PDB:3RAE"
FT HELIX 467..471
FT /evidence="ECO:0007829|PDB:3K9F"
FT HELIX 474..483
FT /evidence="ECO:0007829|PDB:3K9F"
FT HELIX 488..490
FT /evidence="ECO:0007829|PDB:4Z4Q"
FT HELIX 493..495
FT /evidence="ECO:0007829|PDB:4KOE"
FT STRAND 499..504
FT /evidence="ECO:0007829|PDB:3K9F"
FT HELIX 509..524
FT /evidence="ECO:0007829|PDB:3K9F"
FT HELIX 527..531
FT /evidence="ECO:0007829|PDB:3K9F"
FT STRAND 535..538
FT /evidence="ECO:0007829|PDB:3K9F"
FT STRAND 542..547
FT /evidence="ECO:0007829|PDB:3K9F"
FT HELIX 550..552
FT /evidence="ECO:0007829|PDB:3K9F"
FT STRAND 554..558
FT /evidence="ECO:0007829|PDB:3K9F"
FT HELIX 561..570
FT /evidence="ECO:0007829|PDB:3K9F"
FT STRAND 576..579
FT /evidence="ECO:0007829|PDB:3K9F"
FT HELIX 583..585
FT /evidence="ECO:0007829|PDB:3K9F"
FT HELIX 588..595
FT /evidence="ECO:0007829|PDB:3K9F"
FT TURN 598..600
FT /evidence="ECO:0007829|PDB:3K9F"
FT STRAND 603..607
FT /evidence="ECO:0007829|PDB:3K9F"
FT HELIX 612..622
FT /evidence="ECO:0007829|PDB:3K9F"
FT HELIX 627..636
FT /evidence="ECO:0007829|PDB:3K9F"
SQ SEQUENCE 647 AA; 71664 MW; B688A526C9A4E7BA CRC64;
MSKKEININN YNDDAIQVLE GLDAVRKRPG MYIGSTDGAG LHHLVWEIVD NAVDEALSGF
GDRIDVTINK DGSLTVQDHG RGMPTGMHAM GIPTVEVIFT ILHAGGKFGQ GGYKTSGGLH
GVGSSVVNAL SSWLEVEITR DGAVYKQRFE NGGKPVTTLK KIGTAPKSKT GTKVTFMPDA
TIFSTTDFKY NTISERLNES AFLLKNVTLS LTDKRTNEAI EFHYENGVQD FVSYLNEDKE
ILTPVLYFEG EDNGFQVEVA LQYNDGFSDN ILSFVNNVRT KDGGTHETGL KSAITKVMND
YARKTGLLKE KDKNLEGSDY REGLAAVLSI LVPEEHLQFE GQTKDKLGSP LARPVVDGIV
ADKLTFFLME NGELASNLIR KAIKARDARE AARKARDESR NGKKNKKDKG LLSGKLTPAQ
SKNPAKNELY LVEGDSAGGS AKQGRDRKFQ AILPLRGKVV NTAKAKMADI LKNEEINTMI
YTIGAGVGAD FSIEDANYDK IIIMTDADTD GAHIQTLLLT FFYRYMRPLV EAGHVYIALP
PLYKMSKGKG KKEEVAYAWT DGELEELRKQ FGKGATLQRY KGLGEMNADQ LWETTMNPET
RTLIRVTIED LARAERRVNV LMGDKVEPRR KWIEDNVKFT LEETTVF
