P21645 (LPXD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
Short name=UDP-3-O-(3-OHC14)-GlcN N-acyltransferase
EC=2.3.1.191

Alternative name(s):
Protein FirA
Rifampicin resistance protein

Gene names

Name:	lpxD
Synonyms:	firA, omsA
Ordered Locus Names:	b0179, JW0174

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	341 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the N-acylation of UDP-3-O-(hydroxymyristoyl)glucosamine using 3-hydroxymyristoyl-ACP as the acyl donor. Is involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. Prefers R-3-hydroxymyristoyl-ACP over R-3-hydroxypalmitoyl-ACP as the acyl donor in vitro, which is consistent with the structure of E.coli lipid A that contains over 95% (R)-3-hydroxymyristate at the 2 and 2' positions. Ref.8 Ref.11
Catalytic activity	(3R)-3-hydroxymyristoyl-[acyl-carrier-protein] + UDP-3-O-((3R)-hydroxymyristoyl)-alpha-D-glucosamine = UDP-2,3-bis(O-(3R)-3-hydroxymyristoyl)-alpha-D-glucosamine + a holo-[acyl-carrier-protein]. Ref.8 Ref.10 Ref.11
Enzyme regulation	Inhibited by divalent cations such as Ca2+ and Mg2+. Ref.10
Pathway	Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 3/6. HAMAP MF_00523
Subunit structure	Homotrimer. Ref.10 Ref.11
Sequence similarities	Belongs to the transferase hexapeptide repeat family. LpxD subfamily.
Caution	Was originally thought to be involved in transcription.
Biophysicochemical properties	Kinetic parameters: kcat is 23 sec(-1). KM=2.5 µM for UDP-3-O-((3R)-hydroxymyristoyl)-alpha-D-glucosamine Ref.10 KM=3.2 µM for (3R)-3-hydroxymyristoyl-ACP

Ontologies

Keywords
Biological process	Antibiotic resistance Lipid A biosynthesis Lipid synthesis
Domain	Repeat
Molecular function	Acyltransferase Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	lipid A biosynthetic process Inferred from mutant phenotype Ref.9. Source: EcoliWiki response to antibiotic Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	N-acyltransferase activity Inferred from direct assay Ref.9. Source: EcoliWiki
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.1

Chain

2 – 341

340

UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase HAMAP MF_00523

PRO_0000059669

Sites

Active site

239

1

Proton acceptor Ref.10

Site

290

1

Involved in determining the hydroxyacyl-ACP selectivity

Experimental info

Mutagenesis

41

1

F → A: 30-fold decrease in affinity for UDP-3-O-((3R)-hydroxymyristoyl)-GlcN and 5-fold decrease in catalytic activity. Ref.10

Mutagenesis

165

1

Q → R in firA200; confers temperature sensitivity and reverses the rifampicin resistance of rpoB mutants. Ref.1

Mutagenesis

172

1

I → F in firA201; confers temperature sensitivity.

Mutagenesis

228

1

G → D in firA200 and firA201; confers temperature sensitivity. Ref.1

Mutagenesis

239

1

H → A: 1000-fold reduction in catalytic activity with very little effect on substrate affinity. Ref.10

Mutagenesis

252

1

G → S in firA200 and firA201; confers temperature sensitivity. Ref.1

Mutagenesis

271

1

S → N in omsA; confers temperature sensitivity. Ref.7

Mutagenesis

276

1

H → A: 30-fold reduction in catalytic activity. Ref.10

Mutagenesis

290

1

M → A: Change in the acyl donor selectivity, showing a preference for 3-hydroxypalmitoyl-ACP over 3-hydroxymyristoyl-ACP as substrate. Produces a lipid A with longer acyl chains. Ref.11

Mutagenesis

292

1

M → A: No change in the acyl donor selectivity. Ref.11

Secondary structure

1

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341

Helix Strand Turn

Details...

Helix

6 – 12

7

Beta strand

16 – 18

3

Turn

31 – 33

3

Beta strand

39 – 41

3

Helix

47 – 50

4

Beta strand

57 – 61

5

Turn

63 – 65

3

Helix

66 – 68

3

Beta strand

73 – 75

3

Helix

79 – 90

12

Beta strand

277 – 279

3

Helix

310 – 321

12

Helix

323 – 337

15

Sequences

	Sequence		Length	Mass (Da)
	P21645 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: B0ADFED5B17C649D	FASTA	341	36,038
	10 20 30 40 50 60 MPSIRLADLA QQLDAELHGD GDIVITGVAS MQSAQTGHIT FMVNPKYREH LGLCQASAVV 70 80 90 100 110 120 MTQDDLPFAK SAALVVKNPY LTYARMAQIL DTTPQPAQNI APSAVIDATA KLGNNVSIGA 130 140 150 160 170 180 NAVIESGVEL GDNVIIGAGC FVGKNSKIGA GSRLWANVTI YHEIQIGQNC LIQSGTVVGA 190 200 210 220 230 240 DGFGYANDRG NWVKIPQIGR VIIGDRVEIG ACTTIDRGAL DDTIIGNGVI IDNQCQIAHN 250 260 270 280 290 300 VVIGDNTAVA GGVIMAGSLK IGRYCMIGGA SVINGHMEIC DKVTVTGMGM VMRPITEPGV 310 320 330 340 YSSGIPLQPN KVWRKTAALV MNIDDMSKRL KSLERKVNQQ D

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and nucleotide sequence of the firA gene and the firA200(Ts) allele from Escherichia coli." Dicker I.B., Seetharam S.R. J. Bacteriol. 173:334-344(1991) [PubMed: 1987124] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-15, MUTAGENESIS OF GLN-165; GLY-228 AND GLY-252. Strain: K12 / MG1655 / ATCC 47076.
[2]	"Systematic sequencing of the Escherichia coli genome: analysis of the 4.0 - 6.0 min (189,987 - 281,416bp) region." Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T., Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S., Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K. Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"Sequence of minutes 4-25 of Escherichia coli." Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W. Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"What is known about the structure and function of the Escherichia coli protein FirA?" Dicker I.B., Seetharam S.R. Mol. Microbiol. 6:817-823(1992) [PubMed: 1602961] [Abstract] Cited for: REVIEW.
[7]	"Mutants carrying conditionally lethal mutations in outer membrane genes omsA and firA (ssc) are phenotypically similar, and omsA is allelic to firA." Vuorio R., Vaara M. J. Bacteriol. 174:7090-7097(1992) [PubMed: 1429432] [Abstract] Cited for: MUTAGENESIS OF SER-271.
[8]	"Defective biosynthesis of the lipid A component of temperature-sensitive firA (omsA) mutant of Escherichia coli." Helander I.M., Lindner B., Seydel U., Vaara M. Eur. J. Biochem. 212:363-369(1993) [PubMed: 8444173] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, CHARACTERIZATION.
[9]	"The firA gene of Escherichia coli encodes UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase. The third step of endotoxin biosynthesis." Kelly T.M., Stachula S.A., Raetz C.R.H., Anderson M.S. J. Biol. Chem. 268:19866-19874(1993) [PubMed: 8366125] [Abstract] Cited for: CHARACTERIZATION.
[10]	"Steady-state kinetics and mechanism of LpxD, the N-acyltransferase of lipid A biosynthesis." Bartling C.M., Raetz C.R. Biochemistry 47:5290-5302(2008) [PubMed: 18422345] [Abstract] Cited for: CATALYTIC ACTIVITY, ENZYME REGULATION, KINETIC PARAMETERS, SUBUNIT, REACTION MECHANISM, ACTIVE SITE, MUTAGENESIS OF PHE-41; HIS-239 AND HIS-276. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[11]	"Crystal structure and acyl chain selectivity of Escherichia coli LpxD, the N-acyltransferase of lipid A biosynthesis." Bartling C.M., Raetz C.R. Biochemistry 48:8672-8683(2009) [PubMed: 19655786] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, SUBUNIT, CATALYTIC MECHANISM, MUTAGENESIS OF MET-290 AND MET-292. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X54797 Genomic DNA. Translation: CAA38568.1.
U70214 Genomic DNA. Translation: AAB08608.1.
U00096 Genomic DNA. Translation: AAC73290.1.
AP009048 Genomic DNA. Translation: BAA77854.1.

PIR

S13729.

RefSeq

NP_414721.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3EH0	X-ray	2.60	A/B/C	1-341	[»]

ProteinModelPortal

P21645.

SMR

P21645. Positions 1-341.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10124N.

IntAct

P21645. 55 interactions.

MINT

MINT-1218299.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000000537; EBESCP00000000537; EBESCG00000000453.
EBESCT00000000538; EBESCP00000000538; EBESCG00000000453.
EBESCT00000000539; EBESCP00000000539; EBESCG00000000453.
EBESCT00000015704; EBESCP00000014995; EBESCG00000014764.

GeneID

944882.

GenomeReviews

Gene locus JW0174 in contig AP009048_GR.
Gene locus b0179 in contig U00096_GR.

KEGG

ecj:JW0174.
eco:b0179.

PATRIC

32115469. VBIEscCol129921_0186.

Organism-specific databases

EchoBASE

EB0312.

EcoGene

EG10316. lpxD.

Phylogenomic databases

eggNOG

COG1044.

GeneTree

EBGT00050000010008.

HOGENOM

HBG469615.

OMA

CFVGKNT.

PhylomeDB

P21645.

ProtClustDB

PRK00892.

Enzyme and pathway databases

BioCyc

EcoCyc:UDPHYDROXYMYRGLUCOSAMNACETYLTRANS-MONO.
MetaCyc:UDPHYDROXYMYRGLUCOSAMNACETYLTRANS-MONO.

Gene expression databases

Genevestigator

P21645.

Family and domain databases

HAMAP

MF_00523. LpxD.
[Tree]

InterPro

IPR001451. Hexapep_transf.
IPR018357. Hexapep_transf_CS.
IPR011004. Trimer_LpxA-like.
IPR007691. UDP-3-O_GlcNAc_AcTrfase.
IPR020573. UDP_GlcNAc_AcTrfase_non-rep.
[Graphical view]

KO

K02536.

Pfam

PF00132. Hexapep. 3 hits.
PF04613. LpxD. 1 hit.
[Graphical view]

SUPFAM

SSF51161. Trimer_LpxA_like. 1 hit.

TIGRFAMs

TIGR01853. Lipid_A_lpxD. 1 hit.

PROSITE

PS00101. HEXAPEP_TRANSFERASES. 4 hits.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

LPXD_ECOLI

Accession

Primary (citable) accession number: P21645

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1991
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 105 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program