ENCAP_THEMA
ID ENCAP_THEMA Reviewed; 265 AA.
AC Q9WZP2;
DT 22-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT 22-JUL-2008, sequence version 2.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=Type 1 encapsulin shell protein {ECO:0000303|PubMed:19172747};
DE AltName: Full=Maritimacin {ECO:0000303|PubMed:11210524};
DE EC=3.4.-.- {ECO:0000269|PubMed:9872409};
DE AltName: Full=Thermotoga bacteriocin {ECO:0000303|PubMed:9872409};
GN Name=enc {ECO:0000305}; OrderedLocusNames=TM_0785;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [2]
RP PROTEIN SEQUENCE OF 1-15, PROTEASE ACTIVITY, CATALYTIC ACTIVITY, ACTIVITY
RP REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND SUBCELLULAR
RP LOCATION.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=9872409; DOI=10.1016/s0014-5793(98)01451-3;
RA Hicks P.M., Rinker K.D., Baker J.R., Kelly R.M.;
RT "Homomultimeric protease in the hyperthermophilic bacterium Thermotoga
RT maritima has structural and amino acid sequence homology to bacteriocins in
RT mesophilic bacteria.";
RL FEBS Lett. 440:393-398(1998).
RN [3]
RP PROTEIN NAME, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=11210524; DOI=10.1016/s0076-6879(01)30397-x;
RA Hicks P.M., Chang L.S., Kelly R.M.;
RT "Homomultimeric protease and putative bacteriocin homolog from Thermotoga
RT maritima.";
RL Methods Enzymol. 330:455-460(2001).
RN [4]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION, AND
RP BIOTECHNOLOGY.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=27224728; DOI=10.1021/acs.biochem.6b00294;
RA Cassidy-Amstutz C., Oltrogge L., Going C.C., Lee A., Teng P.,
RA Quintanilla D., East-Seletsky A., Williams E.R., Savage D.F.;
RT "Identification of a Minimal Peptide Tag for in Vivo and in Vitro Loading
RT of Encapsulin.";
RL Biochemistry 55:3461-3468(2016).
RN [5]
RP FUNCTION, SUBCELLULAR LOCATION, DOMAIN, BIOTECHNOLOGY, AND MUTAGENESIS OF
RP 182-LYS--LEU-190 AND 184-GLU--PRO-189.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=30376298; DOI=10.1021/acssynbio.8b00295;
RA Williams E.M., Jung S.M., Coffman J.L., Lutz S.;
RT "Pore Engineering for Enhanced Mass Transport in Encapsulin
RT Nanocompartments.";
RL ACS Synth. Biol. 7:2514-2517(2018).
RN [6]
RP FUNCTION, SUBCELLULAR LOCATION, DOMAIN, BIOTECHNOLOGY, AND MUTAGENESIS OF
RP 182-LYS--LEU-190.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=33769792; DOI=10.1021/acssynbio.0c00636;
RA Jenkins M.C., Lutz S.;
RT "Encapsulin Nanocontainers as Versatile Scaffolds for the Development of
RT Artificial Metabolons.";
RL ACS Synth. Biol. 10:857-869(2021).
RN [7]
RP CLASSIFICATION.
RX PubMed=34362927; DOI=10.1038/s41467-021-25071-y;
RA Andreas M.P., Giessen T.W.;
RT "Large-scale computational discovery and analysis of virus-derived
RT microbial nanocompartments.";
RL Nat. Commun. 12:4748-4748(2021).
RN [8] {ECO:0007744|PDB:3DKT}
RP X-RAY CRYSTALLOGRAPHY (3.10 ANGSTROMS), FUNCTION, SUBUNIT, SUBCELLULAR
RP LOCATION, AND DOMAIN.
RX PubMed=19172747; DOI=10.1038/nsmb.1473;
RA Sutter M., Boehringer D., Gutmann S., Gunther S., Prangishvili D.,
RA Loessner M.J., Stetter K.O., Weber-Ban E., Ban N.;
RT "Structural basis of enzyme encapsulation into a bacterial
RT nanocompartment.";
RL Nat. Struct. Mol. Biol. 15:939-947(2008).
RN [9] {ECO:0007744|PDB:7K5W}
RP STRUCTURE BY ELECTRON MICROSCOPY (2.87 ANGSTROMS) IN COMPLEX WITH
RP ARTIFICIAL CARGO, FUNCTION, SUBUNIT, SUBCELLULAR LOCATION, AND
RP BIOTECHNOLOGY.
RX PubMed=32961724; DOI=10.3390/biom10091342;
RA Xiong X., Sun C., Vago F.S., Klose T., Zhu J., Jiang W.;
RT "Cryo-EM Structure of Heterologous Protein Complex Loaded Thermotoga
RT Maritima Encapsulin Capsid.";
RL Biomolecules 10:0-0(2020).
RN [10] {ECO:0007744|PDB:6WKV}
RP STRUCTURE BY ELECTRON MICROSCOPY (2.99 ANGSTROMS) OF 11 ANGSTROMS PORE
RP MUTANT.
RA Williams E., Zhao H., Jenkins M., Juneja P., Lutz S.;
RT "Cryo-EM structure of engineered variant of the Encapsulin from Thermotoga
RT maritima (TmE).";
RL Submitted (APR-2020) to the PDB data bank.
RN [11] {ECO:0007744|PDB:7KQ5}
RP STRUCTURE BY ELECTRON MICROSCOPY (2.00 ANGSTROMS) IN COMPLEX WITH FLAVIN
RP LIGAND, FUNCTION, PROBABLE FMN COFACTOR, SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=33953921; DOI=10.1107/s2052252521001949;
RA Wiryaman T., Toor N.;
RT "Cryo-EM structure of a thermostable bacterial nanocompartment.";
RL IUCrJ 8:342-350(2021).
RN [12] {ECO:0007744|PDB:7MU1}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.30 ANGSTROMS) OF 1-264 IN COMPLEX WITH
RP FMN, FMN COFACTOR, SUBUNIT, SUBCELLULAR LOCATION, AND MUTAGENESIS OF
RP TRP-87.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=34815415; DOI=10.1038/s41598-021-01932-w;
RA LaFrance B.J., Cassidy-Amstutz C., Nichols R.J., Oltrogge L.M., Nogales E.,
RA Savage D.F.;
RT "The encapsulin from Thermotoga maritima is a flavoprotein with a symmetry
RT matched ferritin-like cargo protein.";
RL Sci. Rep. 11:22810-22810(2021).
CC -!- FUNCTION: Shell component of a type 1 encapsulin nanocompartment.
CC Assembles into proteinaceous shells 23-24 nm in diameter with 2-2.5 nm
CC thick walls. Cargo protein Flp (ferritin-like protein, may store iron)
CC is targeted to the interior via its C-terminal extension; empty intact
CC shells can be isolated in the absence of cargo protein
CC (PubMed:19172747, PubMed:27224728, PubMed:32961724, PubMed:30376298,
CC PubMed:33769792, PubMed:33953921, PubMed:34815415). Fe(2+) may be able
CC to pass though the 5-fold and dimer channels in the protein shell
CC (Probable). {ECO:0000269|PubMed:19172747, ECO:0000269|PubMed:27224728,
CC ECO:0000269|PubMed:30376298, ECO:0000269|PubMed:32961724,
CC ECO:0000269|PubMed:33769792, ECO:0000269|PubMed:33953921,
CC ECO:0000269|PubMed:34815415, ECO:0000305|PubMed:33953921}.
CC -!- FUNCTION: Protease that exhibits activity toward chymotrypsin and
CC trypsin substrates (PubMed:9872409, PubMed:11210524). Probably does not
CC have antibacterial activity (Probable). {ECO:0000269|PubMed:11210524,
CC ECO:0000269|PubMed:9872409, ECO:0000305|PubMed:19172747}.
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000269|PubMed:33953921, ECO:0000269|PubMed:34815415};
CC Note=A flavin ligand is bound near the 3-fold axis channel; FMN is
CC consistent with the observed density, absorbance data and mass
CC spectrometry. {ECO:0000269|PubMed:33953921,
CC ECO:0000269|PubMed:34815415};
CC -!- ACTIVITY REGULATION: Proteolysis activated by calcium and cobalt.
CC {ECO:0000269|PubMed:9872409}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH for protease activity is 7.1 (PubMed:11210524,
CC PubMed:9872409). Nanocompartments are stable from pH 4-12, they
CC reversibly disassemble at pH 1 and pH 13 (PubMed:27224728).
CC {ECO:0000269|PubMed:11210524, ECO:0000269|PubMed:27224728,
CC ECO:0000269|PubMed:9872409};
CC Temperature dependence:
CC Optimum temperature for protease activity is 90-93 degrees Celsius.
CC {ECO:0000269|PubMed:11210524, ECO:0000269|PubMed:9872409};
CC -!- SUBUNIT: Homomultimeric (PubMed:9872409). This encapsulin
CC nanocompartment is formed by 60 subunits; monomers form 12 pentamers
CC which assemble to form shells. There are 12 pores where the pentamers
CC meet as well as 3-fold axis channels and dimer channels; none are
CC larger than 3-4 Angstroms in diameter. The N-terminus of the protein is
CC inside the shell, the C-terminus is outside.
CC {ECO:0000269|PubMed:19172747, ECO:0000269|PubMed:30376298,
CC ECO:0000269|PubMed:32961724, ECO:0000269|PubMed:33769792,
CC ECO:0000269|PubMed:33953921, ECO:0000269|PubMed:34815415,
CC ECO:0000269|PubMed:9872409}.
CC -!- SUBCELLULAR LOCATION: Encapsulin nanocompartment
CC {ECO:0000269|PubMed:19172747, ECO:0000269|PubMed:27224728,
CC ECO:0000269|PubMed:30376298, ECO:0000269|PubMed:32961724,
CC ECO:0000269|PubMed:33769792, ECO:0000269|PubMed:33953921,
CC ECO:0000269|PubMed:34815415, ECO:0000305|PubMed:9872409}. Note=Globular
CC particles 19-20 nm, with 60-80 nm long tails (Probable). Shells are 23-
CC 24 nm in diameter, walls are 2.0-2.5 nm thick (PubMed:19172747).
CC {ECO:0000269|PubMed:19172747, ECO:0000305|PubMed:9872409}.
CC -!- DOMAIN: Has 3 domains; a discontinuous peripheral domain (P, 13-39, 76-
CC 133, 221-254), an elongated loop (E, 53-73) and the discontinuous axial
CC domain (A, 137-216 and 259-263). The E-loop forms contacts between two
CC subunits, while the A domain mediates contacts in the 5-fold interface
CC (PubMed:19172747). Pores are formed by residues 184-189, pore size can
CC be modified by mutagenesis (PubMed:30376298, PubMed:33769792).
CC {ECO:0000269|PubMed:19172747, ECO:0000269|PubMed:30376298,
CC ECO:0000269|PubMed:33769792}.
CC -!- BIOTECHNOLOGY: Foreign proteins can be targeted to ectopic
CC nanocompartments in E.coli upon coexpression with a construct using the
CC 15 C-terminal residues of Flp (AC Q9WZP3), tested with GFP. There are
CC at most 20 GFP per compartment. Empty nanocompartments can be
CC disassembled by extreme pH or by 7 M guanidine hydrochloride (GuHCl);
CC only reassembly from GuHCl-dissociated compartments allows
CC incorporation of targeted cargo (PubMed:27224728). The central pore in
CC the pentamer can be enlarged by modifying the pore-forming loop
CC (residues 184-189), which allows transport of larger metabolites than
CC wild-type pores (PubMed:30376298). Artificial metabolons made by
CC targeting proteins to the outside and inside of the nanocompartment
CC have also been made in E.coli; increasing pore size increases metabolic
CC flux (PubMed:33769792). Foreign proteins targeted to nanocompartments
CC have been purified and characterized from insect cells. By C-terminally
CC tagging only IDM1 of A.thaliana, all 6 components of the IDM complex
CC were targeted to the nanocompartment (PubMed:32961724).
CC {ECO:0000269|PubMed:27224728, ECO:0000269|PubMed:30376298,
CC ECO:0000269|PubMed:32961724, ECO:0000269|PubMed:33769792}.
CC -!- MISCELLANEOUS: Shows substantial structural similarity to gp5 of the
CC HK97 viral capsid; while the sequence homology is weak, it suggests
CC this protein may have evolved from a viral capsid protein.
CC {ECO:0000305|PubMed:19172747}.
CC -!- SIMILARITY: Belongs to the encapsulin family. Family 1 subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD35867.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AE000512; AAD35867.1; ALT_FRAME; Genomic_DNA.
DR PIR; B72333; B72333.
DR RefSeq; NP_228594.1; NC_000853.1.
DR RefSeq; WP_004080898.1; NZ_CP011107.1.
DR PDB; 3DKT; X-ray; 3.10 A; A/B/C/D/E/F/G/H/I/J=1-265.
DR PDB; 6WKV; EM; 2.99 A; 0/1/2/3/4/5/6/7/8/9/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T=1-265.
DR PDB; 7K5W; EM; 2.87 A; A=1-265.
DR PDB; 7KQ5; EM; 2.00 A; A=1-265.
DR PDB; 7LII; EM; 3.55 A; A=1-265.
DR PDB; 7LIJ; EM; 2.84 A; A=1-265.
DR PDB; 7LIK; EM; 2.91 A; A=1-265.
DR PDB; 7LIL; EM; 2.84 A; A=1-265.
DR PDB; 7LIM; EM; 2.75 A; A=1-265.
DR PDB; 7LIS; EM; 2.96 A; A=1-265.
DR PDB; 7LIT; EM; 2.53 A; A=1-265.
DR PDB; 7MU1; EM; 3.30 A; A=1-264.
DR PDBsum; 3DKT; -.
DR PDBsum; 6WKV; -.
DR PDBsum; 7K5W; -.
DR PDBsum; 7KQ5; -.
DR PDBsum; 7LII; -.
DR PDBsum; 7LIJ; -.
DR PDBsum; 7LIK; -.
DR PDBsum; 7LIL; -.
DR PDBsum; 7LIM; -.
DR PDBsum; 7LIS; -.
DR PDBsum; 7LIT; -.
DR PDBsum; 7MU1; -.
DR AlphaFoldDB; Q9WZP2; -.
DR SMR; Q9WZP2; -.
DR IntAct; Q9WZP2; 1.
DR STRING; 243274.THEMA_00725; -.
DR MEROPS; U56.001; -.
DR EnsemblBacteria; AAD35867; AAD35867; TM_0785.
DR KEGG; tma:TM0785; -.
DR PATRIC; fig|243274.5.peg.797; -.
DR eggNOG; COG1659; Bacteria.
DR InParanoid; Q9WZP2; -.
DR OMA; DSDWQPV; -.
DR BRENDA; 1.16.3.1; 6331.
DR BRENDA; 3.4.21.1; 6331.
DR EvolutionaryTrace; Q9WZP2; -.
DR Proteomes; UP000008183; Chromosome.
DR GO; GO:0140737; C:encapsulin nanocompartment; IDA:UniProtKB.
DR GO; GO:0008233; F:peptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0006879; P:cellular iron ion homeostasis; IEA:UniProtKB-KW.
DR GO; GO:0006811; P:ion transport; IEA:UniProtKB-KW.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR InterPro; IPR007544; Linocin_M18.
DR Pfam; PF04454; Linocin_M18; 1.
DR PIRSF; PIRSF019254; CFP29; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Encapsulin nanocompartment;
KW Flavoprotein; FMN; Hydrolase; Ion transport; Iron; Iron storage;
KW Iron transport; Protease; Reference proteome; Transport.
FT CHAIN 1..265
FT /note="Type 1 encapsulin shell protein"
FT /id="PRO_0000343950"
FT REGION 184..189
FT /note="Pore-forming loop"
FT /evidence="ECO:0000269|PubMed:30376298,
FT ECO:0000269|PubMed:33769792"
FT BINDING 79..81
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000305|PubMed:33953921,
FT ECO:0007744|PDB:7KQ5"
FT BINDING 87
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:34815415,
FT ECO:0000305|PubMed:33953921, ECO:0007744|PDB:7KQ5,
FT ECO:0007744|PDB:7MU1"
FT BINDING 90..94
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:34815415,
FT ECO:0007744|PDB:7MU1"
FT BINDING 235
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000305|PubMed:33953921,
FT ECO:0007744|PDB:7KQ5"
FT MUTAGEN 87
FT /note="W->E: Loss of flavin-binding. No change in iron
FT storage or iron release under aerobic or anaerobic
FT conditions."
FT /evidence="ECO:0000269|PubMed:34815415"
FT MUTAGEN 182..190
FT /note="KEEAGHYPL->G: Makes few, fragmented
FT nanocompartments."
FT /evidence="ECO:0000269|PubMed:30376298"
FT MUTAGEN 182..190
FT /note="KEEAGHYPL->GG: Forms about 11 Angstroms pore,
FT nanocompartments appear normal. Increased metabolic flux
FT across the pore."
FT /evidence="ECO:0000269|PubMed:30376298,
FT ECO:0000269|PubMed:33769792, ECO:0007744|PDB:6WKV"
FT MUTAGEN 184..189
FT /note="EAGHYP->AA: Forms about 6 Angstroms pore,
FT nanocompartments appear normal."
FT /evidence="ECO:0000269|PubMed:30376298"
FT MUTAGEN 184..189
FT /note="EAGHYP->AAAA: Forms about 5 Angstroms pore,
FT nanocompartments appear normal."
FT /evidence="ECO:0000269|PubMed:30376298"
FT MUTAGEN 184..189
FT /note="EAGHYP->AAAAAA: Still makes about 3 Angstroms pore,
FT nanocompartments appear normal."
FT /evidence="ECO:0000269|PubMed:30376298"
FT MUTAGEN 184..189
FT /note="Missing: Makes few, fragmented nanocompartments."
FT /evidence="ECO:0000269|PubMed:30376298"
FT HELIX 2..4
FT /evidence="ECO:0007829|PDB:7KQ5"
FT HELIX 6..8
FT /evidence="ECO:0007829|PDB:7KQ5"
FT HELIX 13..30
FT /evidence="ECO:0007829|PDB:7KQ5"
FT HELIX 33..35
FT /evidence="ECO:0007829|PDB:7KQ5"
FT STRAND 37..40
FT /evidence="ECO:0007829|PDB:7KQ5"
FT STRAND 49..57
FT /evidence="ECO:0007829|PDB:7KQ5"
FT STRAND 68..74
FT /evidence="ECO:0007829|PDB:7KQ5"
FT STRAND 76..85
FT /evidence="ECO:0007829|PDB:7KQ5"
FT HELIX 86..90
FT /evidence="ECO:0007829|PDB:7KQ5"
FT TURN 91..95
FT /evidence="ECO:0007829|PDB:7KQ5"
FT HELIX 102..121
FT /evidence="ECO:0007829|PDB:7KQ5"
FT TURN 124..127
FT /evidence="ECO:0007829|PDB:7KQ5"
FT HELIX 131..133
FT /evidence="ECO:0007829|PDB:7KQ5"
FT HELIX 135..137
FT /evidence="ECO:0007829|PDB:7KQ5"
FT STRAND 138..140
FT /evidence="ECO:0007829|PDB:7KQ5"
FT HELIX 145..161
FT /evidence="ECO:0007829|PDB:7KQ5"
FT STRAND 168..173
FT /evidence="ECO:0007829|PDB:7KQ5"
FT HELIX 174..183
FT /evidence="ECO:0007829|PDB:7KQ5"
FT STRAND 184..188
FT /evidence="ECO:0007829|PDB:3DKT"
FT HELIX 190..197
FT /evidence="ECO:0007829|PDB:7KQ5"
FT TURN 198..200
FT /evidence="ECO:0007829|PDB:7K5W"
FT STRAND 202..208
FT /evidence="ECO:0007829|PDB:7KQ5"
FT STRAND 210..216
FT /evidence="ECO:0007829|PDB:7KQ5"
FT STRAND 218..237
FT /evidence="ECO:0007829|PDB:7KQ5"
FT STRAND 239..255
FT /evidence="ECO:0007829|PDB:7KQ5"
FT HELIX 257..259
FT /evidence="ECO:0007829|PDB:7KQ5"
FT STRAND 260..264
FT /evidence="ECO:0007829|PDB:7KQ5"
SQ SEQUENCE 265 AA; 30478 MW; 062B867B75CDA155 CRC64;
MEFLKRSFAP LTEKQWQEID NRAREIFKTQ LYGRKFVDVE GPYGWEYAAH PLGEVEVLSD
ENEVVKWGLR KSLPLIELRA TFTLDLWELD NLERGKPNVD LSSLEETVRK VAEFEDEVIF
RGCEKSGVKG LLSFEERKIE CGSTPKDLLE AIVRALSIFS KDGIEGPYTL VINTDRWINF
LKEEAGHYPL EKRVEECLRG GKIITTPRIE DALVVSERGG DFKLILGQDL SIGYEDREKD
AVRLFITETF TFQVVNPEAL ILLKF
