XECC_XANP2
ID XECC_XANP2 Reviewed; 523 AA.
AC Q56839; A7IPY2;
DT 16-JAN-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=2-oxopropyl-CoM reductase, carboxylating {ECO:0000305};
DE EC=1.8.1.5 {ECO:0000269|PubMed:10411892};
DE AltName: Full=2-ketopropyl-coenzyme M oxidoreductase/carboxylase {ECO:0000303|PubMed:12390015};
DE AltName: Full=Aliphatic epoxide carboxylation component II;
DE AltName: Full=Epoxide carboxylase component II {ECO:0000303|PubMed:9150202};
DE AltName: Full=NADPH:2-ketopropyl-CoM oxidoreductase/carboxylase {ECO:0000303|PubMed:10411892};
DE Short=2-KPCC {ECO:0000303|PubMed:12524213};
GN Name=xecC {ECO:0000303|PubMed:12524213}; OrderedLocusNames=Xaut_4867;
OS Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2).
OG Plasmid pXAUT01.
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Xanthobacteraceae; Xanthobacter.
OX NCBI_TaxID=78245;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC BAA-1158 / Py2;
RX PubMed=7704278; DOI=10.1099/13500872-141-2-477;
RA Swaving J., Weijers C.A.G.M., van Ooyen A.J.J., de Bont J.A.M.;
RT "Complementation of Xanthobacter Py2 mutants in epoxyalkane degradation;
RT expression and nucleotide sequence of the complementing DNA fragment.";
RL Microbiology 141:477-484(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-1158 / Py2;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Hammon N.,
RA Israni S., Dalin E., Tice H., Pitluck S., Sims D., Brettin T., Bruce D.,
RA Detter J.C., Han C., Tapia R., Brainard J., Schmutz J., Larimer F.,
RA Land M., Hauser L., Kyrpides N., Kim E., Ensigns S.A., Richardson P.;
RT "Complete sequence of plasmid pXAUT01 of Xanthobacter autotrophicus Py2.";
RL Submitted (JUL-2007) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP FUNCTION, COFACTOR, PATHWAY, AND SUBUNIT.
RC STRAIN=ATCC BAA-1158 / Py2;
RX PubMed=9150202; DOI=10.1128/jb.179.10.3110-3115.1997;
RA Allen J.R., Ensign S.A.;
RT "Characterization of three protein components required for functional
RT reconstitution of the epoxide carboxylase multienzyme complex from
RT Xanthobacter strain Py2.";
RL J. Bacteriol. 179:3110-3115(1997).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, PATHWAY, AND SUBUNIT.
RC STRAIN=ATCC BAA-1158 / Py2;
RX PubMed=10411892; DOI=10.1073/pnas.96.15.8432;
RA Allen J.R., Clark D.D., Krum J.G., Ensign S.A.;
RT "A role for coenzyme M (2-mercaptoethanesulfonic acid) in a bacterial
RT pathway of aliphatic epoxide carboxylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:8432-8437(1999).
RN [5]
RP ACTIVITY REGULATION.
RC STRAIN=ATCC BAA-1158 / Py2;
RX PubMed=20551308; DOI=10.1074/jbc.m110.144410;
RA Boyd J.M., Clark D.D., Kofoed M.A., Ensign S.A.;
RT "Mechanism of inhibition of aliphatic epoxide carboxylation by the coenzyme
RT M analog 2-bromoethanesulfonate.";
RL J. Biol. Chem. 285:25232-25242(2010).
RN [6]
RP REVIEW.
RX PubMed=12524213; DOI=10.1146/annurev.biochem.72.121801.161820;
RA Ensign S.A., Allen J.R.;
RT "Aliphatic epoxide carboxylation.";
RL Annu. Rev. Biochem. 72:55-76(2003).
RN [7] {ECO:0007744|PDB:1MO9, ECO:0007744|PDB:1MOK}
RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEXES WITH
RP 2-OXOPROPYL-COENZYME M AND FAD, SUBUNIT, DOMAIN, AND DISULFIDE BOND.
RC STRAIN=ATCC BAA-1158 / Py2;
RX PubMed=12390015; DOI=10.1021/bi026580p;
RA Nocek B., Jang S.B., Jeong M.S., Clark D.D., Ensign S.A., Peters J.W.;
RT "Structural basis for CO2 fixation by a novel member of the disulfide
RT oxidoreductase family of enzymes, 2-ketopropyl-coenzyme M
RT oxidoreductase/carboxylase.";
RL Biochemistry 41:12907-12913(2002).
RN [8] {ECO:0007744|PDB:2C3C, ECO:0007744|PDB:2C3D}
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEXES WITH COENZYME M; FAD
RP AND NADP, DOMAIN, DISULFIDE BOND, AND REACTION MECHANISM.
RC STRAIN=ATCC BAA-1158 / Py2;
RX PubMed=16388586; DOI=10.1021/bi051518o;
RA Pandey A.S., Nocek B., Clark D.D., Ensign S.A., Peters J.W.;
RT "Mechanistic implications of the structure of the mixed-disulfide
RT intermediate of the disulfide oxidoreductase, 2-ketopropyl-coenzyme M
RT oxidoreductase/carboxylase.";
RL Biochemistry 45:113-120(2006).
RN [9] {ECO:0007744|PDB:3Q6J}
RP X-RAY CRYSTALLOGRAPHY (1.92 ANGSTROMS) IN COMPLEX WITH 2-OXOPROPYL-COENZYME
RP M; COENZYME M; FAD; CARBON DIOXIDE; MAGNESIUM AND NADP, AND REACTION
RP MECHANISM.
RC STRAIN=ATCC BAA-1158 / Py2;
RX PubMed=21192936; DOI=10.1016/j.febslet.2010.12.035;
RA Pandey A.S., Mulder D.W., Ensign S.A., Peters J.W.;
RT "Structural basis for carbon dioxide binding by 2-ketopropyl coenzyme M
RT oxidoreductase/carboxylase.";
RL FEBS Lett. 585:459-464(2011).
CC -!- FUNCTION: Involved in aliphatic epoxide carboxylation (PubMed:10411892,
CC PubMed:9150202). Catalyzes the reductive cleavage of the thioether bond
CC of 2-oxopropyl-coenzyme M (2-KPC), and the subsequent carboxylation of
CC the ketopropyl cleavage product, yielding the products acetoacetate and
CC free coenzyme M (PubMed:10411892). {ECO:0000269|PubMed:10411892,
CC ECO:0000269|PubMed:9150202}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=acetoacetate + coenzyme M + NADP(+) = 2-oxopropyl-coenzyme M +
CC CO2 + NADPH; Xref=Rhea:RHEA:16977, ChEBI:CHEBI:13705,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:57552, ChEBI:CHEBI:57783,
CC ChEBI:CHEBI:58319, ChEBI:CHEBI:58349; EC=1.8.1.5;
CC Evidence={ECO:0000269|PubMed:10411892};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:16979;
CC Evidence={ECO:0000269|PubMed:10411892};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:9150202};
CC Note=Binds 1 FAD per subunit. {ECO:0000269|PubMed:9150202};
CC -!- ACTIVITY REGULATION: Inhibited (at 40%) by the coenzyme M analog 2-
CC bromoethanesulfonate (BES). BES is a time-dependent inactivator of
CC dithiothreitol-reduced 2-KPCC, where the redox active cysteines are in
CC the free thiol forms. BES does not inactivate air-oxidized 2-KPCC,
CC where the redox active cysteine pair is in the disulfide form. BES
CC specifically alkylates the interchange thiol that facilitates thioether
CC bond cleavage and enolacetone formation during catalysis.
CC {ECO:0000269|PubMed:20551308}.
CC -!- PATHWAY: Alkene metabolism; propylene degradation.
CC {ECO:0000269|PubMed:10411892, ECO:0000269|PubMed:9150202}.
CC -!- SUBUNIT: Homodimer (PubMed:9150202, PubMed:12390015). Component II of
CC the aliphatic epoxide carboxylation complex together with components I,
CC III and IV (PubMed:9150202, PubMed:10411892).
CC {ECO:0000269|PubMed:10411892, ECO:0000269|PubMed:12390015,
CC ECO:0000269|PubMed:9150202}.
CC -!- DOMAIN: Contains three domains, the FAD binding domain, the NADPH
CC binding domain, and the dimerization domain (PubMed:12390015). The
CC binding of the substrate induces a conformational change that results
CC in the sequestration of the substrate at the dimer interface
CC (PubMed:12390015, PubMed:16388586). {ECO:0000269|PubMed:12390015,
CC ECO:0000269|PubMed:16388586}.
CC -!- MISCELLANEOUS: The active site is a redox-active disulfide bond
CC (PubMed:12390015, PubMed:16388586). 2-KPC reduction and carboxylation
CC assumes the formation of a mixed disulfide between the interchange
CC thiol (Cys-82) and coenzyme M (PubMed:16388586).
CC {ECO:0000269|PubMed:12390015, ECO:0000269|PubMed:16388586}.
CC -!- SIMILARITY: Belongs to the class-I pyridine nucleotide-disulfide
CC oxidoreductase family. {ECO:0000305}.
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DR EMBL; X79863; CAA56243.1; -; Genomic_DNA.
DR EMBL; CP000782; ABS70078.1; -; Genomic_DNA.
DR PIR; S47053; S47053.
DR RefSeq; WP_011992982.1; NC_009717.1.
DR PDB; 1MO9; X-ray; 1.65 A; A/B=1-523.
DR PDB; 1MOK; X-ray; 2.80 A; A/B/C/D=1-523.
DR PDB; 2C3C; X-ray; 2.15 A; A/B=1-523.
DR PDB; 2C3D; X-ray; 2.15 A; A/B=1-523.
DR PDB; 3Q6J; X-ray; 1.92 A; A/B=1-523.
DR PDB; 7MGN; X-ray; 1.80 A; A/B=1-523.
DR PDB; 7MGO; X-ray; 1.85 A; A/B=1-523.
DR PDBsum; 1MO9; -.
DR PDBsum; 1MOK; -.
DR PDBsum; 2C3C; -.
DR PDBsum; 2C3D; -.
DR PDBsum; 3Q6J; -.
DR PDBsum; 7MGN; -.
DR PDBsum; 7MGO; -.
DR AlphaFoldDB; Q56839; -.
DR SMR; Q56839; -.
DR MINT; Q56839; -.
DR STRING; 78245.Xaut_4867; -.
DR DrugBank; DB03163; 2-oxopropyl-CoM.
DR DrugBank; DB03147; Flavin adenine dinucleotide.
DR EnsemblBacteria; ABS70078; ABS70078; Xaut_4867.
DR KEGG; xau:Xaut_4867; -.
DR eggNOG; COG1249; Bacteria.
DR HOGENOM; CLU_520687_0_0_5; -.
DR OrthoDB; 267896at2; -.
DR PhylomeDB; Q56839; -.
DR BioCyc; MetaCyc:MON-8022; -.
DR BRENDA; 1.8.1.5; 1641.
DR UniPathway; UPA00776; -.
DR EvolutionaryTrace; Q56839; -.
DR Proteomes; UP000002417; Plasmid pXAUT01.
DR GO; GO:0050628; F:2-oxopropyl-CoM reductase (carboxylating) activity; IEA:UniProtKB-EC.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
DR GO; GO:0045454; P:cell redox homeostasis; IEA:InterPro.
DR GO; GO:0042208; P:propylene catabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.30.390.30; -; 1.
DR Gene3D; 3.50.50.60; -; 2.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR023753; FAD/NAD-binding_dom.
DR InterPro; IPR016156; FAD/NAD-linked_Rdtase_dimer_sf.
DR InterPro; IPR004099; Pyr_nucl-diS_OxRdtase_dimer.
DR Pfam; PF07992; Pyr_redox_2; 1.
DR Pfam; PF02852; Pyr_redox_dim; 1.
DR SUPFAM; SSF51905; SSF51905; 1.
DR SUPFAM; SSF55424; SSF55424; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Disulfide bond; FAD; Flavoprotein; NADP; Oxidoreductase;
KW Plasmid; Redox-active center; Reference proteome.
FT CHAIN 1..523
FT /note="2-oxopropyl-CoM reductase, carboxylating"
FT /id="PRO_0000068006"
FT BINDING 53..54
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:12390015,
FT ECO:0000269|PubMed:16388586, ECO:0000269|PubMed:21192936,
FT ECO:0007744|PDB:1MO9, ECO:0007744|PDB:1MOK,
FT ECO:0007744|PDB:2C3C, ECO:0007744|PDB:2C3D,
FT ECO:0007744|PDB:3Q6J"
FT BINDING 56
FT /ligand="2-oxopropyl-coenzyme M"
FT /ligand_id="ChEBI:CHEBI:57552"
FT /evidence="ECO:0000269|PubMed:12390015,
FT ECO:0000269|PubMed:21192936, ECO:0000305|PubMed:16388586,
FT ECO:0007744|PDB:1MO9, ECO:0007744|PDB:3Q6J"
FT BINDING 81
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:12390015,
FT ECO:0000269|PubMed:16388586, ECO:0000269|PubMed:21192936,
FT ECO:0007744|PDB:1MO9, ECO:0007744|PDB:1MOK,
FT ECO:0007744|PDB:2C3C, ECO:0007744|PDB:2C3D,
FT ECO:0007744|PDB:3Q6J"
FT BINDING 82
FT /ligand="2-oxopropyl-coenzyme M"
FT /ligand_id="ChEBI:CHEBI:57552"
FT /evidence="ECO:0000269|PubMed:21192936,
FT ECO:0000305|PubMed:16388586, ECO:0007744|PDB:3Q6J"
FT BINDING 158
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:12390015,
FT ECO:0000269|PubMed:16388586, ECO:0000269|PubMed:21192936,
FT ECO:0007744|PDB:1MO9, ECO:0007744|PDB:1MOK,
FT ECO:0007744|PDB:2C3C, ECO:0007744|PDB:2C3D,
FT ECO:0007744|PDB:3Q6J"
FT BINDING 222..225
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:16388586,
FT ECO:0000269|PubMed:21192936, ECO:0007744|PDB:2C3C,
FT ECO:0007744|PDB:3Q6J"
FT BINDING 245..246
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:16388586,
FT ECO:0000269|PubMed:21192936, ECO:0007744|PDB:2C3C,
FT ECO:0007744|PDB:3Q6J"
FT BINDING 353
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:12390015,
FT ECO:0000269|PubMed:16388586, ECO:0000269|PubMed:21192936,
FT ECO:0007744|PDB:1MO9, ECO:0007744|PDB:1MOK,
FT ECO:0007744|PDB:2C3C, ECO:0007744|PDB:2C3D,
FT ECO:0007744|PDB:3Q6J"
FT BINDING 360
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:16388586,
FT ECO:0000269|PubMed:21192936, ECO:0007744|PDB:2C3C,
FT ECO:0007744|PDB:3Q6J"
FT BINDING 361
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:12390015,
FT ECO:0000269|PubMed:16388586, ECO:0000269|PubMed:21192936,
FT ECO:0007744|PDB:1MO9, ECO:0007744|PDB:1MOK,
FT ECO:0007744|PDB:2C3C, ECO:0007744|PDB:2C3D,
FT ECO:0007744|PDB:3Q6J"
FT BINDING 365
FT /ligand="2-oxopropyl-coenzyme M"
FT /ligand_id="ChEBI:CHEBI:57552"
FT /evidence="ECO:0000269|PubMed:12390015,
FT ECO:0000269|PubMed:21192936, ECO:0000305|PubMed:16388586,
FT ECO:0007744|PDB:1MO9, ECO:0007744|PDB:3Q6J"
FT BINDING 501
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:12390015,
FT ECO:0000269|PubMed:16388586, ECO:0000269|PubMed:21192936,
FT ECO:0007744|PDB:1MO9, ECO:0007744|PDB:1MOK,
FT ECO:0007744|PDB:2C3C, ECO:0007744|PDB:2C3D,
FT ECO:0007744|PDB:3Q6J"
FT DISULFID 82..87
FT /note="Redox-active"
FT /evidence="ECO:0000269|PubMed:12390015,
FT ECO:0000269|PubMed:16388586"
FT STRAND 3..5
FT /evidence="ECO:0007829|PDB:1MO9"
FT TURN 7..9
FT /evidence="ECO:0007829|PDB:1MOK"
FT HELIX 13..25
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 32..35
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 44..49
FT /evidence="ECO:0007829|PDB:1MO9"
FT HELIX 53..64
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 69..79
FT /evidence="ECO:0007829|PDB:1MO9"
FT HELIX 81..85
FT /evidence="ECO:0007829|PDB:1MO9"
FT HELIX 87..105
FT /evidence="ECO:0007829|PDB:1MO9"
FT TURN 106..108
FT /evidence="ECO:0007829|PDB:1MO9"
FT HELIX 122..132
FT /evidence="ECO:0007829|PDB:1MO9"
FT HELIX 134..146
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 152..156
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 159..162
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 165..168
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 171..176
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 178..180
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 184..186
FT /evidence="ECO:0007829|PDB:7MGN"
FT TURN 192..195
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 199..201
FT /evidence="ECO:0007829|PDB:1MO9"
FT HELIX 202..208
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 215..220
FT /evidence="ECO:0007829|PDB:1MO9"
FT HELIX 224..235
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 239..243
FT /evidence="ECO:0007829|PDB:1MO9"
FT TURN 248..251
FT /evidence="ECO:0007829|PDB:1MO9"
FT HELIX 255..267
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 271..275
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 277..283
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 287..296
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 299..304
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 308..310
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 314..316
FT /evidence="ECO:0007829|PDB:7MGN"
FT HELIX 319..325
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 348..350
FT /evidence="ECO:0007829|PDB:1MO9"
FT HELIX 352..355
FT /evidence="ECO:0007829|PDB:1MO9"
FT HELIX 361..375
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 389..401
FT /evidence="ECO:0007829|PDB:1MO9"
FT HELIX 404..409
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 414..420
FT /evidence="ECO:0007829|PDB:1MO9"
FT TURN 424..427
FT /evidence="ECO:0007829|PDB:1MO9"
FT TURN 435..437
FT /evidence="ECO:0007829|PDB:1MO9"
FT HELIX 438..442
FT /evidence="ECO:0007829|PDB:1MO9"
FT TURN 444..446
FT /evidence="ECO:0007829|PDB:1MO9"
FT HELIX 447..450
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 452..458
FT /evidence="ECO:0007829|PDB:1MO9"
FT TURN 459..461
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 463..473
FT /evidence="ECO:0007829|PDB:1MO9"
FT HELIX 475..486
FT /evidence="ECO:0007829|PDB:1MO9"
FT HELIX 491..495
FT /evidence="ECO:0007829|PDB:1MO9"
FT HELIX 507..514
FT /evidence="ECO:0007829|PDB:1MO9"
FT STRAND 517..519
FT /evidence="ECO:0007829|PDB:7MGN"
SQ SEQUENCE 523 AA; 57348 MW; 01962978B88E2015 CRC64;
MKVWNARNDH LTINQWATRI DEILEAPDGG EVIYNVDEND PREYDAIFIG GGAAGRFGSA
YLRAMGGRQL IVDRWPFLGG SCPHNACVPH HLFSDCAAEL MLARTFSGQY WFPDMTEKVV
GIKEVVDLFR AGRNGPHGIM NFQSKEQLNL EYILNCPAKV IDNHTVEAAG KVFKAKNLIL
AVGAGPGTLD VPGVNAKGVF DHATLVEELD YEPGSTVVVV GGSKTAVEYG CFFNATGRRT
VMLVRTEPLK LIKDNETRAY VLDRMKEQGM EIISGSNVTR IEEDANGRVQ AVVAMTPNGE
MRIETDFVFL GLGEQPRSAE LAKILGLDLG PKGEVLVNEY LQTSVPNVYA VGDLIGGPME
MFKARKSGCY AARNVMGEKI SYTPKNYPDF LHTHYEVSFL GMGEEEARAA GHEIVTIKMP
PDTENGLNVA LPASDRTMLY AFGKGTAHMS GFQKIVIDAK TRKVLGAHHV GYGAKDAFQY
LNVLIKQGLT VDELGDMDEL FLNPTHFIQL SRLRAGSKNL VSL
