COAD_ECOLI
ID COAD_ECOLI Reviewed; 159 AA.
AC P0A6I6; P23875; Q2M7U8;
DT 29-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 29-MAR-2005, sequence version 1.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=Phosphopantetheine adenylyltransferase {ECO:0000255|HAMAP-Rule:MF_00151, ECO:0000303|PubMed:10480925};
DE EC=2.7.7.3 {ECO:0000255|HAMAP-Rule:MF_00151, ECO:0000269|PubMed:10480925, ECO:0000269|PubMed:17873050};
DE AltName: Full=Dephospho-CoA pyrophosphorylase {ECO:0000255|HAMAP-Rule:MF_00151};
DE AltName: Full=Pantetheine-phosphate adenylyltransferase {ECO:0000255|HAMAP-Rule:MF_00151};
DE Short=PPAT {ECO:0000255|HAMAP-Rule:MF_00151, ECO:0000303|PubMed:10480925};
GN Name=coaD {ECO:0000255|HAMAP-Rule:MF_00151, ECO:0000303|PubMed:10480925};
GN Synonyms=kdtB {ECO:0000303|PubMed:1577693}, yicA;
GN OrderedLocusNames=b3634, JW3609;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=2033061; DOI=10.1016/s0021-9258(18)92875-9;
RA Clementz T., Raetz C.R.H.;
RT "A gene coding for 3-deoxy-D-manno-octulosonic-acid transferase in
RT Escherichia coli. Identification, mapping, cloning, and sequencing.";
RL J. Biol. Chem. 266:9687-9696(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8041620; DOI=10.1093/nar/22.13.2576;
RA Sofia H.J., Burland V., Daniels D.L., Plunkett G. III, Blattner F.R.;
RT "Analysis of the Escherichia coli genome. V. DNA sequence of the region
RT from 76.0 to 81.5 minutes.";
RL Nucleic Acids Res. 22:2576-2586(1994).
RN [3]
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 [4]
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 [5]
RP PROTEIN SEQUENCE OF 1-10, FUNCTION, CATALYTIC ACTIVITY, POSSIBLE ACTIVITY
RP REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND COA-BINDING.
RC STRAIN=K12 / JM101 / ATCC 33876 / DSM 3948 / NCIMB 11926;
RX PubMed=10480925; DOI=10.1074/jbc.274.38.27105;
RA Geerlof A., Lewendon A., Shaw W.V.;
RT "Purification and characterization of phosphopantetheine
RT adenylyltransferase from Escherichia coli.";
RL J. Biol. Chem. 274:27105-27111(1999).
RN [6]
RP GENETIC CHARACTERIZATION.
RC STRAIN=K12;
RX PubMed=1577693; DOI=10.1128/jb.174.10.3250-3260.1992;
RA Roncero C., Casadaban M.J.;
RT "Genetic analysis of the genes involved in synthesis of the
RT lipopolysaccharide core in Escherichia coli K-12: three operons in the rfa
RT locus.";
RL J. Bacteriol. 174:3250-3260(1992).
RN [7]
RP ACTIVITY REGULATION.
RX PubMed=12750020; DOI=10.1016/s0223-5234(03)00047-3;
RA Zhao L., Allanson N.M., Thomson S.P., Maclean J.K., Barker J.J.,
RA Primrose W.U., Tyler P.D., Lewendon A.;
RT "Inhibitors of phosphopantetheine adenylyltransferase.";
RL Eur. J. Med. Chem. 38:345-349(2003).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL
RP PROPERTIES, SUBUNIT, AND COA-BINDING.
RC STRAIN=K12 / JL4;
RX PubMed=17873050; DOI=10.1128/jb.00732-07;
RA Miller J.R., Ohren J., Sarver R.W., Mueller W.T., de Dreu P., Case H.,
RA Thanabal V.;
RT "Phosphopantetheine adenylyltransferase from Escherichia coli:
RT investigation of the kinetic mechanism and role in regulation of coenzyme A
RT biosynthesis.";
RL J. Bacteriol. 189:8196-8205(2007).
RN [9]
RP ACTIVITY REGULATION, AND INHIBITOR SCREENING.
RX PubMed=20486930; DOI=10.1111/j.1747-0285.2010.00957.x;
RA Miller J.R., Thanabal V., Melnick M.M., Lall M., Donovan C., Sarver R.W.,
RA Lee D.Y., Ohren J., Emerson D.;
RT "The use of biochemical and biophysical tools for triage of high-throughput
RT screening hits - A case study with Escherichia coli phosphopantetheine
RT adenylyltransferase.";
RL Chem. Biol. Drug Des. 75:444-454(2010).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH 3'-DEPHOSPHO-COA, AND
RP SUBUNIT.
RX PubMed=10205156; DOI=10.1093/emboj/18.8.2021;
RA Izard T., Geerlof A.;
RT "The crystal structure of a novel bacterial adenylyltransferase reveals
RT half of sites reactivity.";
RL EMBO J. 18:2021-2030(1999).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (1.63 ANGSTROMS) IN COMPLEXES WITH ATP OR
RP 4'-PHOSPHOPANTETHEINE, COFACTOR, REACTION MECHANISM, SITE, AND SUBUNIT.
RX PubMed=11812124; DOI=10.1006/jmbi.2001.5272;
RA Izard T.;
RT "The crystal structures of phosphopantetheine adenylyltransferase with
RT bound substrates reveal the enzyme's catalytic mechanism.";
RL J. Mol. Biol. 315:487-495(2002).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (1.78 ANGSTROMS) IN COMPLEX WITH COENZYME A AND
RP 4'-PHOSPHOPANTETHEINE, ACTIVITY REGULATION, AND SUBUNIT.
RX PubMed=12837781; DOI=10.1128/jb.185.14.4074-4080.2003;
RA Izard T.;
RT "A novel adenylate binding site confers phosphopantetheine
RT adenylyltransferase interactions with coenzyme A.";
RL J. Bacteriol. 185:4074-4080(2003).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS).
RX PubMed=27130242; DOI=10.1007/s10858-016-0032-2;
RA Proudfoot A., Frank A.O., Ruggiu F., Mamo M., Lingel A.;
RT "Facilitating unambiguous NMR assignments and enabling higher probe density
RT through selective labeling of all methyl containing amino acids.";
RL J. Biomol. NMR 65:15-27(2016).
CC -!- FUNCTION: Reversibly transfers an adenylyl group from ATP to 4'-
CC phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate
CC (PubMed:10480925, PubMed:17873050). CoA is not a substrate for the
CC enzyme (PubMed:10480925). {ECO:0000255|HAMAP-Rule:MF_00151,
CC ECO:0000269|PubMed:10480925, ECO:0000269|PubMed:17873050}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-4'-phosphopantetheine + ATP + H(+) = 3'-dephospho-CoA +
CC diphosphate; Xref=Rhea:RHEA:19801, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:57328,
CC ChEBI:CHEBI:61723; EC=2.7.7.3; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00151, ECO:0000269|PubMed:10480925,
CC ECO:0000269|PubMed:17873050};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:11812124};
CC Note=Crystallized in the absence of Mg(2+), the catalytic metal is not
CC bound by the protein but probably by non-esterified oxygen atoms from
CC ATP and/or ordered H(2)O (PubMed:11812124).
CC {ECO:0000305|PubMed:11812124};
CC -!- ACTIVITY REGULATION: Feedback inhibited by CoA, which is competitive
CC with ATP, 4'-phosphopantetheine and 3'-dephospho-CoA (PubMed:17873050,
CC PubMed:10480925). Binds 0.5 CoA tightly per monomer in the same
CC position as 3'-dephospho-CoA but in a different fashion
CC (PubMed:12837781, PubMed:17873050). Is inhibited by the very potent and
CC specific inhibitor PTX042695 dipeptide, with an IC(50) of 6 nM, a
CC compound which has no activity against porcine PPAT (PubMed:12750020).
CC A series of pyrazoloquinolones were also characterized as ATP-
CC competitive inhibitors of PPAT (PubMed:20486930).
CC {ECO:0000269|PubMed:12750020, ECO:0000269|PubMed:12837781,
CC ECO:0000269|PubMed:17873050, ECO:0000269|PubMed:20486930,
CC ECO:0000305|PubMed:10480925}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=7.0 uM for 3'-dephospho-CoA {ECO:0000269|PubMed:10480925};
CC KM=17.0 uM for 3'-dephospho-CoA {ECO:0000269|PubMed:17873050};
CC KM=0.22 mM for diphosphate {ECO:0000269|PubMed:10480925};
CC KM=0.23 mM for diphosphate {ECO:0000269|PubMed:17873050};
CC KM=220 uM for ATP {ECO:0000269|PubMed:17873050};
CC KM=4.7 uM for 4'-phosphopantetheine {ECO:0000269|PubMed:17873050};
CC Note=kcat is 1.37 sec(-1) for the forward reaction, with ATP and
CC pantetheine 4'-phosphate as substrates (PubMed:17873050). kcat is 3.3
CC sec(-1) for the reverse reaction, with diphosphate and 3'-dephospho-
CC CoA as substrates (PubMed:10480925). kcat is 1.37 sec(-1) for the
CC reverse reaction, with diphosphate and 3'-dephospho-CoA as substrates
CC (PubMed:17873050). {ECO:0000269|PubMed:10480925,
CC ECO:0000269|PubMed:17873050};
CC pH dependence:
CC Optimum pH is 6.9. {ECO:0000269|PubMed:10480925};
CC -!- PATHWAY: Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-
CC pantothenate: step 4/5. {ECO:0000255|HAMAP-Rule:MF_00151}.
CC -!- SUBUNIT: Homohexamer, a dimerized trimer with a solvent channel through
CC the middle (PubMed:10480925, PubMed:10205156, PubMed:11812124,
CC PubMed:12837781, PubMed:17873050). In crystals only 1 trimer is seen to
CC bind substrate/product at a time (PubMed:10205156, PubMed:11812124).
CC {ECO:0000269|PubMed:10205156, ECO:0000269|PubMed:10480925,
CC ECO:0000269|PubMed:11812124, ECO:0000269|PubMed:12837781,
CC ECO:0000269|PubMed:17873050}.
CC -!- INTERACTION:
CC P0A6I6; P60723: rplD; NbExp=2; IntAct=EBI-553173, EBI-545597;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00151}.
CC -!- MISCELLANEOUS: The crystal structures in complex with substrates
CC suggest the enzyme stabilizes the transition state but the functional
CC groups of the enzyme are not directly involved in reaction catalysis.
CC {ECO:0000305|PubMed:11812124}.
CC -!- SIMILARITY: Belongs to the bacterial CoaD family. {ECO:0000255|HAMAP-
CC Rule:MF_00151}.
CC -!- CAUTION: Was originally thought to have an essential function in
CC lipopolysaccharide biosynthesis. {ECO:0000305|PubMed:1577693}.
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DR EMBL; M60670; AAA24044.1; -; Genomic_DNA.
DR EMBL; M86305; AAA03746.1; -; Genomic_DNA.
DR EMBL; U00039; AAB18611.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76658.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77658.1; -; Genomic_DNA.
DR PIR; JU0468; JU0468.
DR RefSeq; NP_418091.1; NC_000913.3.
DR RefSeq; WP_001171866.1; NZ_STEB01000024.1.
DR PDB; 1B6T; X-ray; 1.80 A; A/B=1-159.
DR PDB; 1GN8; X-ray; 1.83 A; A/B=1-159.
DR PDB; 1H1T; X-ray; 1.78 A; A/B=1-159.
DR PDB; 1QJC; X-ray; 1.63 A; A/B=2-159.
DR PDB; 5JBN; X-ray; 1.45 A; A/B=1-159.
DR PDB; 6B7A; X-ray; 1.99 A; A/B=1-159.
DR PDB; 6B7B; X-ray; 1.98 A; A/B=1-159.
DR PDB; 6B7C; X-ray; 1.56 A; A/B=1-159.
DR PDB; 6B7D; X-ray; 1.80 A; A/B=1-159.
DR PDB; 6B7E; X-ray; 2.10 A; A/B=1-159.
DR PDB; 6B7F; X-ray; 2.56 A; A/B=1-159.
DR PDB; 6CCK; X-ray; 1.61 A; A/B=1-159.
DR PDB; 6CCL; X-ray; 1.77 A; A/B=1-159.
DR PDB; 6CCM; X-ray; 1.79 A; A/B=1-159.
DR PDB; 6CCN; X-ray; 1.87 A; A/B=1-159.
DR PDB; 6CCO; X-ray; 1.82 A; A/B=1-159.
DR PDB; 6CCQ; X-ray; 1.92 A; A/B=1-159.
DR PDB; 6CCS; X-ray; 2.06 A; A/B=1-159.
DR PDB; 6CHL; X-ray; 2.20 A; A/B=1-159.
DR PDB; 6CHM; X-ray; 2.28 A; A/B=1-159.
DR PDB; 6CHN; X-ray; 2.03 A; A/B=1-159.
DR PDB; 6CHO; X-ray; 1.85 A; A/B=1-159.
DR PDB; 6CHP; X-ray; 1.94 A; A/B=1-159.
DR PDB; 6CHQ; X-ray; 1.79 A; A/B=1-159.
DR PDB; 6CKW; X-ray; 2.06 A; A/B=1-159.
DR PDBsum; 1B6T; -.
DR PDBsum; 1GN8; -.
DR PDBsum; 1H1T; -.
DR PDBsum; 1QJC; -.
DR PDBsum; 5JBN; -.
DR PDBsum; 6B7A; -.
DR PDBsum; 6B7B; -.
DR PDBsum; 6B7C; -.
DR PDBsum; 6B7D; -.
DR PDBsum; 6B7E; -.
DR PDBsum; 6B7F; -.
DR PDBsum; 6CCK; -.
DR PDBsum; 6CCL; -.
DR PDBsum; 6CCM; -.
DR PDBsum; 6CCN; -.
DR PDBsum; 6CCO; -.
DR PDBsum; 6CCQ; -.
DR PDBsum; 6CCS; -.
DR PDBsum; 6CHL; -.
DR PDBsum; 6CHM; -.
DR PDBsum; 6CHN; -.
DR PDBsum; 6CHO; -.
DR PDBsum; 6CHP; -.
DR PDBsum; 6CHQ; -.
DR PDBsum; 6CKW; -.
DR AlphaFoldDB; P0A6I6; -.
DR SMR; P0A6I6; -.
DR BioGRID; 4263379; 238.
DR DIP; DIP-35966N; -.
DR IntAct; P0A6I6; 10.
DR STRING; 511145.b3634; -.
DR BindingDB; P0A6I6; -.
DR ChEMBL; CHEMBL4523175; -.
DR jPOST; P0A6I6; -.
DR PaxDb; P0A6I6; -.
DR PRIDE; P0A6I6; -.
DR EnsemblBacteria; AAC76658; AAC76658; b3634.
DR EnsemblBacteria; BAE77658; BAE77658; BAE77658.
DR GeneID; 67417636; -.
DR GeneID; 947386; -.
DR KEGG; ecj:JW3609; -.
DR KEGG; eco:b3634; -.
DR PATRIC; fig|1411691.4.peg.3072; -.
DR EchoBASE; EB1176; -.
DR eggNOG; COG0669; Bacteria.
DR HOGENOM; CLU_100149_0_1_6; -.
DR InParanoid; P0A6I6; -.
DR OMA; EFQMALM; -.
DR PhylomeDB; P0A6I6; -.
DR BioCyc; EcoCyc:PANTEPADENYLYLTRAN-MON; -.
DR BioCyc; MetaCyc:PANTEPADENYLYLTRAN-MON; -.
DR BRENDA; 2.7.7.3; 2026.
DR SABIO-RK; P0A6I6; -.
DR UniPathway; UPA00241; UER00355.
DR EvolutionaryTrace; P0A6I6; -.
DR PRO; PR:P0A6I6; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0004595; F:pantetheine-phosphate adenylyltransferase activity; IDA:EcoCyc.
DR GO; GO:0015937; P:coenzyme A biosynthetic process; IDA:EcoCyc.
DR CDD; cd02163; PPAT; 1.
DR Gene3D; 3.40.50.620; -; 1.
DR HAMAP; MF_00151; PPAT_bact; 1.
DR InterPro; IPR004821; Cyt_trans-like.
DR InterPro; IPR001980; PPAT.
DR InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR PANTHER; PTHR21342:SF1; PTHR21342:SF1; 1.
DR Pfam; PF01467; CTP_transf_like; 1.
DR PRINTS; PR01020; LPSBIOSNTHSS.
DR TIGRFAMs; TIGR01510; coaD_prev_kdtB; 1.
DR TIGRFAMs; TIGR00125; cyt_tran_rel; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Coenzyme A biosynthesis; Cytoplasm;
KW Direct protein sequencing; Magnesium; Nucleotide-binding;
KW Nucleotidyltransferase; Reference proteome; Transferase.
FT CHAIN 1..159
FT /note="Phosphopantetheine adenylyltransferase"
FT /id="PRO_0000156204"
FT BINDING 7..11
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:11812124,
FT ECO:0007744|PDB:1GN8"
FT BINDING 10
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11812124,
FT ECO:0000269|PubMed:12837781, ECO:0007744|PDB:1H1T,
FT ECO:0007744|PDB:1QJC"
FT BINDING 18
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:11812124,
FT ECO:0007744|PDB:1GN8"
FT BINDING 42
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11812124,
FT ECO:0000269|PubMed:12837781, ECO:0007744|PDB:1H1T,
FT ECO:0007744|PDB:1QJC"
FT BINDING 74
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11812124,
FT ECO:0000269|PubMed:12837781, ECO:0007744|PDB:1H1T,
FT ECO:0007744|PDB:1QJC"
FT BINDING 88
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11812124,
FT ECO:0007744|PDB:1QJC"
FT BINDING 89..91
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:11812124,
FT ECO:0007744|PDB:1GN8"
FT BINDING 99
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:11812124,
FT ECO:0007744|PDB:1GN8"
FT BINDING 124..130
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:11812124,
FT ECO:0007744|PDB:1GN8"
FT SITE 18
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000305|PubMed:11812124"
FT STRAND 4..9
FT /evidence="ECO:0007829|PDB:5JBN"
FT HELIX 16..28
FT /evidence="ECO:0007829|PDB:5JBN"
FT STRAND 29..37
FT /evidence="ECO:0007829|PDB:5JBN"
FT HELIX 40..42
FT /evidence="ECO:0007829|PDB:5JBN"
FT HELIX 48..58
FT /evidence="ECO:0007829|PDB:5JBN"
FT TURN 59..61
FT /evidence="ECO:0007829|PDB:5JBN"
FT STRAND 65..70
FT /evidence="ECO:0007829|PDB:5JBN"
FT HELIX 74..80
FT /evidence="ECO:0007829|PDB:5JBN"
FT STRAND 85..89
FT /evidence="ECO:0007829|PDB:5JBN"
FT HELIX 96..109
FT /evidence="ECO:0007829|PDB:5JBN"
FT STRAND 113..118
FT /evidence="ECO:0007829|PDB:5JBN"
FT HELIX 122..124
FT /evidence="ECO:0007829|PDB:5JBN"
FT HELIX 129..137
FT /evidence="ECO:0007829|PDB:5JBN"
FT HELIX 143..145
FT /evidence="ECO:0007829|PDB:5JBN"
FT HELIX 148..159
FT /evidence="ECO:0007829|PDB:5JBN"
SQ SEQUENCE 159 AA; 17837 MW; C4D7B8715A061B91 CRC64;
MQKRAIYPGT FDPITNGHID IVTRATQMFD HVILAIAASP SKKPMFTLEE RVALAQQATA
HLGNVEVVGF SDLMANFARN QHATVLIRGL RAVADFEYEM QLAHMNRHLM PELESVFLMP
SKEWSFISSS LVKEVARHQG DVTHFLPENV HQALMAKLA
