LPXI_CAUVC
ID LPXI_CAUVC Reviewed; 280 AA.
AC Q9A716;
DT 05-JUL-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 83.
DE RecName: Full=UDP-2,3-diacylglucosamine pyrophosphatase LpxI {ECO:0000303|PubMed:20608695};
DE EC=3.6.1.54 {ECO:0000269|PubMed:20608695};
DE AltName: Full=UDP-2,3-diacylglucosamine hydrolase LpxI {ECO:0000303|PubMed:20608695};
GN Name=lpxI {ECO:0000303|PubMed:20608695};
GN OrderedLocusNames=CC_1910 {ECO:0000312|EMBL:AAK23885.1};
OS Caulobacter vibrioides (strain ATCC 19089 / CB15) (Caulobacter crescentus).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales;
OC Caulobacteraceae; Caulobacter.
OX NCBI_TaxID=190650;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 19089 / CB15;
RX PubMed=11259647; DOI=10.1073/pnas.061029298;
RA Nierman W.C., Feldblyum T.V., Laub M.T., Paulsen I.T., Nelson K.E.,
RA Eisen J.A., Heidelberg J.F., Alley M.R.K., Ohta N., Maddock J.R.,
RA Potocka I., Nelson W.C., Newton A., Stephens C., Phadke N.D., Ely B.,
RA DeBoy R.T., Dodson R.J., Durkin A.S., Gwinn M.L., Haft D.H., Kolonay J.F.,
RA Smit J., Craven M.B., Khouri H.M., Shetty J., Berry K.J., Utterback T.R.,
RA Tran K., Wolf A.M., Vamathevan J.J., Ermolaeva M.D., White O.,
RA Salzberg S.L., Venter J.C., Shapiro L., Fraser C.M.;
RT "Complete genome sequence of Caulobacter crescentus.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:4136-4141(2001).
RN [2]
RP IDENTIFICATION, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL
RP PROPERTIES, SUBSTRATE SPECIFICITY, ACTIVITY REGULATION, PATHWAY, AND
RP REACTION MECHANISM.
RC STRAIN=ATCC 19089 / CB15;
RX PubMed=20608695; DOI=10.1021/bi1008744;
RA Metzger L.E. IV, Raetz C.R.;
RT "An alternative route for UDP-diacylglucosamine hydrolysis in bacterial
RT lipid A biosynthesis.";
RL Biochemistry 49:6715-6726(2010).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.52 ANGSTROMS) OF WILD-TYPE IN COMPLEX WITH ITS
RP PRODUCT LIPID X AND MUTANT ALA-225 IN COMPLEX WITH SUBSTRATE, SUBUNIT,
RP SUBCELLULAR LOCATION, DOMAIN, AND MUTAGENESIS OF GLU-182; GLU-185; THR-187;
RP ARG-193; GLN-220 AND ASP-225.
RX PubMed=23042606; DOI=10.1038/nsmb.2393;
RA Metzger L.E., Lee J.K., Finer-Moore J.S., Raetz C.R., Stroud R.M.;
RT "LpxI structures reveal how a lipid A precursor is synthesized.";
RL Nat. Struct. Mol. Biol. 19:1132-1138(2012).
CC -!- FUNCTION: Hydrolyzes the pyrophosphate bond of UDP-2,3-
CC diacylglucosamine to form 2,3-diacylglucosamine 1-phosphate (lipid X)
CC and UMP by catalyzing the attack of water at the beta-P atom. Involved
CC in the biosynthesis of lipid A, a phosphorylated glycolipid that
CC anchors the lipopolysaccharide to the outer membrane of the cell. Can
CC functionally complement lpxH deficiency in E.coli. Cannot use CDP-
CC diacylglycerol as substrate. {ECO:0000269|PubMed:20608695}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + UDP-2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-
CC glucosamine = 2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-
CC glucosaminyl 1-phosphate + 2 H(+) + UMP; Xref=Rhea:RHEA:25213,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:57865,
CC ChEBI:CHEBI:57957, ChEBI:CHEBI:78847; EC=3.6.1.54;
CC Evidence={ECO:0000269|PubMed:20608695};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:20608695};
CC Note=To a lesser extent, can also use Mn(2+) or Co(2+).
CC {ECO:0000269|PubMed:20608695};
CC -!- ACTIVITY REGULATION: Inhibited by high concentrations of Cu(2+) and
CC Zn(2+). Completely inhibited by EDTA in vitro.
CC {ECO:0000269|PubMed:20608695}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=105 uM for UDP-2-N,3-O-bis((3R)-3-hydroxytetradecanoyl)-alpha-D-
CC glucosamine {ECO:0000269|PubMed:20608695};
CC Vmax=69 umol/min/mg enzyme {ECO:0000269|PubMed:20608695};
CC pH dependence:
CC Optimum pH is 7-9. The activity is relatively constant between pH 6.5
CC and 9 but declines sharply below pH 6. {ECO:0000269|PubMed:20608695};
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 4/6. {ECO:0000305|PubMed:20608695}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:23042606}.
CC -!- SUBCELLULAR LOCATION: Cell inner membrane
CC {ECO:0000305|PubMed:23042606}; Peripheral membrane protein
CC {ECO:0000305|PubMed:23042606}; Cytoplasmic side
CC {ECO:0000305|PubMed:23042606}.
CC -!- DOMAIN: Consists of two domains: an N-terminal lipid X binding domain
CC (LXD) attached by a flexible linker to a C-terminal catalytic domain
CC (ICD). Binding of UDP-2,3-diacylglucosamine by LpxI induces a
CC conformational switch that brings the catalytic domain close to the
CC lipid-binding domain for specific recognition of the substrate and
CC catalysis. {ECO:0000269|PubMed:23042606}.
CC -!- MISCELLANEOUS: LpxI generates the same products from the same substrate
CC than LpxH but by a different hydrolytic mechanism. LpxH and LpxI share
CC no sequence similarity and show a different taxonomic distribution.
CC {ECO:0000305|PubMed:20608695}.
CC -!- SIMILARITY: Belongs to the LpxI family. {ECO:0000305}.
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DR EMBL; AE005673; AAK23885.1; -; Genomic_DNA.
DR PIR; A87486; A87486.
DR RefSeq; NP_420717.1; NC_002696.2.
DR RefSeq; WP_010919776.1; NC_002696.2.
DR PDB; 4GGM; X-ray; 2.90 A; X=1-280.
DR PDB; 4J6E; X-ray; 2.52 A; A=1-280.
DR PDBsum; 4GGM; -.
DR PDBsum; 4J6E; -.
DR AlphaFoldDB; Q9A716; -.
DR SMR; Q9A716; -.
DR STRING; 190650.CC_1910; -.
DR EnsemblBacteria; AAK23885; AAK23885; CC_1910.
DR KEGG; ccr:CC_1910; -.
DR PATRIC; fig|190650.5.peg.1927; -.
DR eggNOG; COG3494; Bacteria.
DR HOGENOM; CLU_085042_1_0_5; -.
DR OMA; CKPQQDI; -.
DR BioCyc; CAULO:CC1910-MON; -.
DR UniPathway; UPA00359; UER00480.
DR Proteomes; UP000001816; Chromosome.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0008758; F:UDP-2,3-diacylglucosamine hydrolase activity; IDA:UniProtKB.
DR GO; GO:0009245; P:lipid A biosynthetic process; IGI:UniProtKB.
DR Gene3D; 3.40.140.80; -; 1.
DR InterPro; IPR010415; LpxI_C.
DR InterPro; IPR043167; LpxI_C_sf.
DR InterPro; IPR041255; LpxI_N.
DR Pfam; PF06230; LpxI_C; 1.
DR Pfam; PF17930; LpxI_N; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell inner membrane; Cell membrane; Hydrolase;
KW Lipid A biosynthesis; Lipid biosynthesis; Lipid metabolism; Magnesium;
KW Membrane; Reference proteome.
FT CHAIN 1..280
FT /note="UDP-2,3-diacylglucosamine pyrophosphatase LpxI"
FT /id="PRO_0000440978"
FT BINDING 12
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23042606,
FT ECO:0007744|PDB:4J6E"
FT BINDING 74..75
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23042606,
FT ECO:0007744|PDB:4J6E"
FT BINDING 169
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23042606,
FT ECO:0007744|PDB:4J6E"
FT BINDING 187..188
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23042606,
FT ECO:0007744|PDB:4J6E"
FT BINDING 214
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23042606,
FT ECO:0007744|PDB:4J6E"
FT BINDING 226..233
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23042606,
FT ECO:0007744|PDB:4J6E"
FT MUTAGEN 182
FT /note="E->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:23042606"
FT MUTAGEN 185
FT /note="E->A: Highly reduced catalytic activity."
FT /evidence="ECO:0000269|PubMed:23042606"
FT MUTAGEN 187
FT /note="T->A: Highly reduced catalytic activity."
FT /evidence="ECO:0000269|PubMed:23042606"
FT MUTAGEN 193
FT /note="R->A: Wild-type level of catalytic activity."
FT /evidence="ECO:0000269|PubMed:23042606"
FT MUTAGEN 220
FT /note="Q->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:23042606"
FT MUTAGEN 225
FT /note="D->A: Loss of catalytic activity. Still able to bind
FT substrate."
FT /evidence="ECO:0000269|PubMed:23042606"
SQ SEQUENCE 280 AA; 29634 MW; 44659E41CE50A978 CRC64;
MRKLGLIAGG GALPVELASH CEAAGRAFAV MRLRSFADPS LDRYPGADVG IGEFGKIFKA
LRAEGCDVVC FAGNVSRPDF SALMPDARGL KVLPSLIVAA RKGDDALLRR VLDEFEKEGF
EIEGAHEVMG EMTLPRGRLG KVSPAPEHMA DIDKALDVAR EIGRLDIGQG AVVCEGLVLA
VEAQEGTDAM LRRVADLPEA IRGRAERRLG VLAKAPKPIQ ETRVDLPTIG VATIHRAARA
GLAGIVGEAG RLLVVDREAV IAAADDLGLF VLGVDPQERP
