LPXD_ECOLI
ID LPXD_ECOLI Reviewed; 341 AA.
AC P21645;
DT 01-MAY-1991, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 177.
DE RecName: Full=UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase;
DE Short=UDP-3-O-(3-OHC14)-GlcN N-acyltransferase;
DE EC=2.3.1.191 {ECO:0000269|PubMed:18422345, ECO:0000269|PubMed:19655786, ECO:0000269|PubMed:8444173};
DE AltName: Full=Protein FirA;
DE AltName: Full=Rifampicin resistance protein;
DE AltName: Full=UDP-3-O-(3-hydroxytetradecanoyl)glucosamine N-acyltransferase;
GN Name=lpxD; Synonyms=firA, omsA; OrderedLocusNames=b0179, JW0174;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-15, AND
RP MUTAGENESIS OF GLN-165; GLY-228 AND GLY-252.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=1987124; DOI=10.1128/jb.173.1.334-344.1991;
RA Dicker I.B., Seetharam S.R.;
RT "Cloning and nucleotide sequence of the firA gene and the firA200(Ts)
RT allele from Escherichia coli.";
RL J. Bacteriol. 173:334-344(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T.,
RA Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S.,
RA Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K.;
RT "Systematic sequencing of the Escherichia coli genome: analysis of the 4.0
RT - 6.0 min (189,987 - 281,416bp) region.";
RL Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [4]
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 [5]
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 [6]
RP REVIEW.
RX PubMed=1602961; DOI=10.1111/j.1365-2958.1992.tb01532.x;
RA Dicker I.B., Seetharam S.R.;
RT "What is known about the structure and function of the Escherichia coli
RT protein FirA?";
RL Mol. Microbiol. 6:817-823(1992).
RN [7]
RP MUTAGENESIS OF SER-271.
RX PubMed=1429432; DOI=10.1128/jb.174.22.7090-7097.1992;
RA Vuorio R., Vaara M.;
RT "Mutants carrying conditionally lethal mutations in outer membrane genes
RT omsA and firA (ssc) are phenotypically similar, and omsA is allelic to
RT firA.";
RL J. Bacteriol. 174:7090-7097(1992).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, AND CHARACTERIZATION.
RX PubMed=8444173; DOI=10.1111/j.1432-1033.1993.tb17670.x;
RA Helander I.M., Lindner B., Seydel U., Vaara M.;
RT "Defective biosynthesis of the lipid A component of temperature-sensitive
RT firA (omsA) mutant of Escherichia coli.";
RL Eur. J. Biochem. 212:363-369(1993).
RN [9]
RP CHARACTERIZATION.
RX PubMed=8366125; DOI=10.1016/s0021-9258(19)36593-7;
RA Kelly T.M., Stachula S.A., Raetz C.R.H., Anderson M.S.;
RT "The firA gene of Escherichia coli encodes UDP-3-O-(R-3-hydroxymyristoyl)-
RT glucosamine N-acyltransferase. The third step of endotoxin biosynthesis.";
RL J. Biol. Chem. 268:19866-19874(1993).
RN [10]
RP CATALYTIC ACTIVITY, ACTIVITY REGULATION, KINETIC PARAMETERS, SUBUNIT,
RP REACTION MECHANISM, ACTIVE SITE, AND MUTAGENESIS OF PHE-41; HIS-239 AND
RP HIS-276.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=18422345; DOI=10.1021/bi800240r;
RA Bartling C.M., Raetz C.R.;
RT "Steady-state kinetics and mechanism of LpxD, the N-acyltransferase of
RT lipid A biosynthesis.";
RL Biochemistry 47:5290-5302(2008).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP SUBSTRATE SPECIFICITY, SUBUNIT, CATALYTIC MECHANISM, AND MUTAGENESIS OF
RP MET-290 AND MET-292.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=19655786; DOI=10.1021/bi901025v;
RA Bartling C.M., Raetz C.R.;
RT "Crystal structure and acyl chain selectivity of Escherichia coli LpxD, the
RT N-acyltransferase of lipid A biosynthesis.";
RL Biochemistry 48:8672-8683(2009).
CC -!- FUNCTION: Catalyzes the N-acylation of UDP-3-O-
CC (hydroxytetradecanoyl)glucosamine using 3-hydroxytetradecanoyl-ACP as
CC the acyl donor. Is involved in the biosynthesis of lipid A, a
CC phosphorylated glycolipid that anchors the lipopolysaccharide to the
CC outer membrane of the cell. Prefers (3R)-3-hydroxytetradecanoyl-ACP
CC over (3R)-3-hydroxyhexadecanoyl-ACP as the acyl donor in vitro, which
CC is consistent with the structure of E.coli lipid A that contains over
CC 95% (R)-3-hydroxytetradecanoate at the 2 and 2' positions.
CC {ECO:0000269|PubMed:19655786, ECO:0000269|PubMed:8444173}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a (3R)-hydroxyacyl-[ACP] + a UDP-3-O-[(3R)-3-hydroxyacyl]-
CC alpha-D-glucosamine = a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-
CC glucosamine + H(+) + holo-[ACP]; Xref=Rhea:RHEA:53836, Rhea:RHEA-
CC COMP:9685, Rhea:RHEA-COMP:9945, ChEBI:CHEBI:15378, ChEBI:CHEBI:64479,
CC ChEBI:CHEBI:78827, ChEBI:CHEBI:137740, ChEBI:CHEBI:137748;
CC EC=2.3.1.191; Evidence={ECO:0000269|PubMed:18422345,
CC ECO:0000269|PubMed:19655786, ECO:0000269|PubMed:8444173};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(3R)-hydroxytetradecanoyl-[ACP] + UDP-3-O-[(3R)-3-
CC hydroxytetradecanoyl]-alpha-D-glucosamine = H(+) + holo-[ACP] + UDP-
CC 2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosamine;
CC Xref=Rhea:RHEA:17817, Rhea:RHEA-COMP:9646, Rhea:RHEA-COMP:9685,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:64479, ChEBI:CHEBI:71573,
CC ChEBI:CHEBI:78474, ChEBI:CHEBI:78847;
CC Evidence={ECO:0000269|PubMed:18422345, ECO:0000269|PubMed:19655786,
CC ECO:0000269|PubMed:8444173};
CC -!- ACTIVITY REGULATION: Inhibited by divalent cations such as Ca(2+) and
CC Mg(2+). {ECO:0000269|PubMed:18422345}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2.5 uM for UDP-3-O-((3R)-hydroxytetradecanoyl)-alpha-D-glucosamine
CC {ECO:0000269|PubMed:18422345};
CC KM=3.2 uM for (3R)-3-hydroxytetradecanoyl-ACP
CC {ECO:0000269|PubMed:18422345};
CC Note=kcat is 23 sec(-1).;
CC -!- PATHWAY: Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A)
CC from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-
CC acetyl-alpha-D-glucosamine: step 3/6.
CC -!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:18422345,
CC ECO:0000269|PubMed:19655786}.
CC -!- SIMILARITY: Belongs to the transferase hexapeptide repeat family. LpxD
CC subfamily. {ECO:0000305}.
CC -!- CAUTION: Was originally thought to be involved in transcription.
CC {ECO:0000305}.
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DR EMBL; X54797; CAA38568.1; -; Genomic_DNA.
DR EMBL; U70214; AAB08608.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73290.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA77854.1; -; Genomic_DNA.
DR PIR; S13729; S13729.
DR RefSeq; NP_414721.1; NC_000913.3.
DR RefSeq; WP_001139279.1; NZ_STEB01000032.1.
DR PDB; 3EH0; X-ray; 2.60 A; A/B/C=1-341.
DR PDB; 4IHF; X-ray; 2.10 A; A/B/C/D/E/F=3-341.
DR PDB; 4IHG; X-ray; 2.89 A; A/B/C/D/E/F=3-341.
DR PDB; 4IHH; X-ray; 2.13 A; A/B/C/D/E/F=3-341.
DR PDB; 6P83; X-ray; 1.70 A; A/B/C=3-341.
DR PDB; 6P84; X-ray; 1.70 A; A/B/C=3-341.
DR PDB; 6P85; X-ray; 1.90 A; A/B/C=3-341.
DR PDB; 6P86; X-ray; 1.80 A; A/B/C=3-341.
DR PDB; 6P87; X-ray; 1.90 A; A/B/C=3-341.
DR PDB; 6P88; X-ray; 1.70 A; A/B/C=3-341.
DR PDB; 6P89; X-ray; 1.40 A; A/B/C=3-341.
DR PDB; 6P8A; X-ray; 1.80 A; A/B/C=3-341.
DR PDB; 6P8B; X-ray; 2.00 A; A/B/C=3-341.
DR PDBsum; 3EH0; -.
DR PDBsum; 4IHF; -.
DR PDBsum; 4IHG; -.
DR PDBsum; 4IHH; -.
DR PDBsum; 6P83; -.
DR PDBsum; 6P84; -.
DR PDBsum; 6P85; -.
DR PDBsum; 6P86; -.
DR PDBsum; 6P87; -.
DR PDBsum; 6P88; -.
DR PDBsum; 6P89; -.
DR PDBsum; 6P8A; -.
DR PDBsum; 6P8B; -.
DR AlphaFoldDB; P21645; -.
DR SMR; P21645; -.
DR BioGRID; 4259589; 448.
DR DIP; DIP-10124N; -.
DR IntAct; P21645; 56.
DR STRING; 511145.b0179; -.
DR BindingDB; P21645; -.
DR SwissLipids; SLP:000001884; -.
DR jPOST; P21645; -.
DR PaxDb; P21645; -.
DR PRIDE; P21645; -.
DR EnsemblBacteria; AAC73290; AAC73290; b0179.
DR EnsemblBacteria; BAA77854; BAA77854; BAA77854.
DR GeneID; 66671533; -.
DR GeneID; 944882; -.
DR KEGG; ecj:JW0174; -.
DR KEGG; eco:b0179; -.
DR PATRIC; fig|1411691.4.peg.2100; -.
DR EchoBASE; EB0312; -.
DR eggNOG; COG1044; Bacteria.
DR HOGENOM; CLU_049865_0_1_6; -.
DR InParanoid; P21645; -.
DR OMA; QIQIAHN; -.
DR PhylomeDB; P21645; -.
DR BioCyc; EcoCyc:UDPHYDROXYMYRGLUCOSAMNACETYLTRANS-MONO; -.
DR BioCyc; MetaCyc:UDPHYDROXYMYRGLUCOSAMNACETYLTRANS-MONO; -.
DR BRENDA; 2.3.1.191; 2026.
DR SABIO-RK; P21645; -.
DR UniPathway; UPA00359; UER00479.
DR EvolutionaryTrace; P21645; -.
DR PRO; PR:P21645; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:EcoCyc.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0016410; F:N-acyltransferase activity; IDA:EcoliWiki.
DR GO; GO:0103118; F:UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase activity; IDA:EcoCyc.
DR GO; GO:0009245; P:lipid A biosynthetic process; IMP:EcoliWiki.
DR GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
DR CDD; cd03352; LbH_LpxD; 1.
DR HAMAP; MF_00523; LpxD; 1.
DR InterPro; IPR001451; Hexapep.
DR InterPro; IPR018357; Hexapep_transf_CS.
DR InterPro; IPR007691; LpxD.
DR InterPro; IPR011004; Trimer_LpxA-like_sf.
DR InterPro; IPR020573; UDP_GlcNAc_AcTrfase_non-rep.
DR PANTHER; PTHR43378; PTHR43378; 1.
DR Pfam; PF00132; Hexapep; 3.
DR Pfam; PF04613; LpxD; 1.
DR SUPFAM; SSF51161; SSF51161; 1.
DR TIGRFAMs; TIGR01853; lipid_A_lpxD; 1.
DR PROSITE; PS00101; HEXAPEP_TRANSFERASES; 4.
PE 1: Evidence at protein level;
KW 3D-structure; Acyltransferase; Antibiotic resistance;
KW Direct protein sequencing; Lipid A biosynthesis; Lipid biosynthesis;
KW Lipid metabolism; Reference proteome; Repeat; Transferase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:1987124"
FT CHAIN 2..341
FT /note="UDP-3-O-(3-hydroxymyristoyl)glucosamine N-
FT acyltransferase"
FT /id="PRO_0000059669"
FT ACT_SITE 239
FT /note="Proton acceptor"
FT /evidence="ECO:0000269|PubMed:18422345"
FT SITE 290
FT /note="Involved in determining the hydroxyacyl-ACP
FT selectivity"
FT MUTAGEN 41
FT /note="F->A: 30-fold decrease in affinity for UDP-3-O-
FT ((3R)-hydroxytetradecanoyl)-GlcN and 5-fold decrease in
FT catalytic activity."
FT /evidence="ECO:0000269|PubMed:18422345"
FT MUTAGEN 165
FT /note="Q->R: In firA200; confers temperature sensitivity
FT and reverses the rifampicin resistance of rpoB mutants."
FT /evidence="ECO:0000269|PubMed:1987124"
FT MUTAGEN 172
FT /note="I->F: In firA201; confers temperature sensitivity."
FT MUTAGEN 228
FT /note="G->D: In firA200 and firA201; confers temperature
FT sensitivity."
FT /evidence="ECO:0000269|PubMed:1987124"
FT MUTAGEN 239
FT /note="H->A: 1000-fold reduction in catalytic activity with
FT very little effect on substrate affinity."
FT /evidence="ECO:0000269|PubMed:18422345"
FT MUTAGEN 252
FT /note="G->S: In firA200 and firA201; confers temperature
FT sensitivity."
FT /evidence="ECO:0000269|PubMed:1987124"
FT MUTAGEN 271
FT /note="S->N: In omsA; confers temperature sensitivity."
FT /evidence="ECO:0000269|PubMed:1429432"
FT MUTAGEN 276
FT /note="H->A: 30-fold reduction in catalytic activity."
FT /evidence="ECO:0000269|PubMed:18422345"
FT MUTAGEN 290
FT /note="M->A: Change in the acyl donor selectivity, showing
FT a preference for 3-hydroxypalmitoyl-ACP over 3-
FT hydroxytetradecanoyl-ACP as substrate. Produces a lipid A
FT with longer acyl chains."
FT /evidence="ECO:0000269|PubMed:19655786"
FT MUTAGEN 292
FT /note="M->A: No change in the acyl donor selectivity."
FT /evidence="ECO:0000269|PubMed:19655786"
FT HELIX 6..12
FT /evidence="ECO:0007829|PDB:6P89"
FT STRAND 16..19
FT /evidence="ECO:0007829|PDB:6P89"
FT TURN 31..33
FT /evidence="ECO:0007829|PDB:6P89"
FT STRAND 38..41
FT /evidence="ECO:0007829|PDB:6P89"
FT HELIX 45..53
FT /evidence="ECO:0007829|PDB:6P89"
FT STRAND 57..61
FT /evidence="ECO:0007829|PDB:6P89"
FT TURN 63..65
FT /evidence="ECO:0007829|PDB:6P89"
FT HELIX 66..68
FT /evidence="ECO:0007829|PDB:6P89"
FT STRAND 70..75
FT /evidence="ECO:0007829|PDB:6P89"
FT HELIX 79..89
FT /evidence="ECO:0007829|PDB:6P89"
FT STRAND 98..100
FT /evidence="ECO:0007829|PDB:6P89"
FT STRAND 177..179
FT /evidence="ECO:0007829|PDB:6P89"
FT STRAND 185..188
FT /evidence="ECO:0007829|PDB:6P89"
FT STRAND 191..194
FT /evidence="ECO:0007829|PDB:6P89"
FT STRAND 201..203
FT /evidence="ECO:0007829|PDB:6P89"
FT STRAND 214..216
FT /evidence="ECO:0007829|PDB:6P83"
FT STRAND 219..221
FT /evidence="ECO:0007829|PDB:6P89"
FT STRAND 223..225
FT /evidence="ECO:0007829|PDB:6P89"
FT STRAND 259..261
FT /evidence="ECO:0007829|PDB:6P8B"
FT STRAND 275..279
FT /evidence="ECO:0007829|PDB:6P8B"
FT STRAND 283..285
FT /evidence="ECO:0007829|PDB:6P89"
FT STRAND 299..302
FT /evidence="ECO:0007829|PDB:6P89"
FT HELIX 310..321
FT /evidence="ECO:0007829|PDB:6P89"
FT HELIX 323..336
FT /evidence="ECO:0007829|PDB:6P89"
SQ SEQUENCE 341 AA; 36038 MW; B0ADFED5B17C649D CRC64;
MPSIRLADLA QQLDAELHGD GDIVITGVAS MQSAQTGHIT FMVNPKYREH LGLCQASAVV
MTQDDLPFAK SAALVVKNPY LTYARMAQIL DTTPQPAQNI APSAVIDATA KLGNNVSIGA
NAVIESGVEL GDNVIIGAGC FVGKNSKIGA GSRLWANVTI YHEIQIGQNC LIQSGTVVGA
DGFGYANDRG NWVKIPQIGR VIIGDRVEIG ACTTIDRGAL DDTIIGNGVI IDNQCQIAHN
VVIGDNTAVA GGVIMAGSLK IGRYCMIGGA SVINGHMEIC DKVTVTGMGM VMRPITEPGV
YSSGIPLQPN KVWRKTAALV MNIDDMSKRL KSLERKVNQQ D
