LPXH_HAEIN
ID LPXH_HAEIN Reviewed; 237 AA.
AC P44046;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=UDP-2,3-diacylglucosamine hydrolase {ECO:0000255|HAMAP-Rule:MF_00575};
DE EC=3.6.1.54 {ECO:0000255|HAMAP-Rule:MF_00575, ECO:0000269|PubMed:23897835};
DE AltName: Full=UDP-2,3-diacylglucosamine diphosphatase {ECO:0000255|HAMAP-Rule:MF_00575};
DE AltName: Full=UDP-diacylglucosamine pyrophosphohydrolase {ECO:0000303|PubMed:23897835};
GN Name=lpxH {ECO:0000255|HAMAP-Rule:MF_00575, ECO:0000303|PubMed:23897835};
GN OrderedLocusNames=HI_0735;
OS Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales;
OC Pasteurellaceae; Haemophilus.
OX NCBI_TaxID=71421;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 51907 / DSM 11121 / KW20 / Rd;
RX PubMed=7542800; DOI=10.1126/science.7542800;
RA Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F.,
RA Kerlavage A.R., Bult C.J., Tomb J.-F., Dougherty B.A., Merrick J.M.,
RA McKenney K., Sutton G.G., FitzHugh W., Fields C.A., Gocayne J.D.,
RA Scott J.D., Shirley R., Liu L.-I., Glodek A., Kelley J.M., Weidman J.F.,
RA Phillips C.A., Spriggs T., Hedblom E., Cotton M.D., Utterback T.R.,
RA Hanna M.C., Nguyen D.T., Saudek D.M., Brandon R.C., Fine L.D.,
RA Fritchman J.L., Fuhrmann J.L., Geoghagen N.S.M., Gnehm C.L., McDonald L.A.,
RA Small K.V., Fraser C.M., Smith H.O., Venter J.C.;
RT "Whole-genome random sequencing and assembly of Haemophilus influenzae
RT Rd.";
RL Science 269:496-512(1995).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBCELLULAR LOCATION, PATHWAY, AND MUTAGENESIS OF ASP-9; HIS-11; ASP-42;
RP ARG-81; HIS-115; ASP-117 AND HIS-196.
RC STRAIN=ATCC 51907 / DSM 11121 / KW20 / Rd;
RX PubMed=23897835; DOI=10.1074/jbc.m113.497636;
RA Young H.E., Donohue M.P., Smirnova T.I., Smirnov A.I., Zhou P.;
RT "The UDP-diacylglucosamine pyrophosphohydrolase LpxH in lipid A
RT biosynthesis utilizes Mn2+ cluster for catalysis.";
RL J. Biol. Chem. 288:26987-27001(2013).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.55 ANGSTROMS) IN COMPLEX WITH ITS PRODUCT LIPID X
RP AND MANGANESE, COFACTOR, AND REACTION MECHANISM.
RC STRAIN=ATCC 51907 / DSM 11121 / KW20 / Rd;
RX PubMed=27780190; DOI=10.1038/nmicrobiol.2016.154;
RA Cho J., Lee C.J., Zhao J., Young H.E., Zhou P.;
RT "Structure of the essential Haemophilus influenzae UDP-diacylglucosamine
RT pyrophosphohydrolase LpxH in lipid A biosynthesis.";
RL Nat. Microbiol. 1:16154-16154(2016).
CC -!- FUNCTION: Hydrolyzes the pyrophosphate bond of UDP-2,3-
CC diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X)
CC and UMP by catalyzing the attack of water at the alpha-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.
CC {ECO:0000255|HAMAP-Rule:MF_00575, ECO:0000269|PubMed:23897835}.
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:0000255|HAMAP-Rule:MF_00575,
CC ECO:0000269|PubMed:23897835};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:23897835, ECO:0000269|PubMed:27780190};
CC Note=Binds 2 Mn(2+) ions per subunit in a binuclear metal center
CC (PubMed:23897835, PubMed:27780190). May bind a third metal with
CC significantly weaker affinity that might facilitate the catalysis but
CC only binds LpxH in the presence of the substrate (PubMed:23897835).
CC {ECO:0000269|PubMed:23897835, ECO:0000269|PubMed:27780190};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=79.4 uM for UDP-2-N,3-O-bis((3R)-3-hydroxytetradecanoyl)-alpha-D-
CC glucosamine {ECO:0000269|PubMed:23897835};
CC Vmax=18.1 mmol/min/mg enzyme {ECO:0000269|PubMed:23897835};
CC pH dependence:
CC Optimum pH is 7-9.5. Is most active at slightly alkaline pH values
CC and exhibits a sharp decrease in its catalytic activity at low pH.
CC The drop in LpxH activity at acidic pH is not due to enzyme
CC instability as preincubation of the enzyme at low pH does not alter
CC the apparent enzyme activity at the standard condition of pH 8.0.
CC {ECO:0000269|PubMed:23897835};
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:0000255|HAMAP-Rule:MF_00575,
CC ECO:0000305|PubMed:23897835}.
CC -!- SUBCELLULAR LOCATION: Cell inner membrane
CC {ECO:0000305|PubMed:23897835}; Peripheral membrane protein
CC {ECO:0000269|PubMed:23897835}; Cytoplasmic side
CC {ECO:0000305|PubMed:23897835}. Cytoplasm {ECO:0000269|PubMed:23897835}.
CC -!- SIMILARITY: Belongs to the LpxH family. {ECO:0000255|HAMAP-
CC Rule:MF_00575}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; L42023; AAC22394.1; -; Genomic_DNA.
DR PIR; A64013; A64013.
DR RefSeq; NP_438894.1; NC_000907.1.
DR RefSeq; WP_005693139.1; NC_000907.1.
DR PDB; 5K8K; X-ray; 2.55 A; A=1-237.
DR PDBsum; 5K8K; -.
DR AlphaFoldDB; P44046; -.
DR SMR; P44046; -.
DR STRING; 71421.HI_0735; -.
DR DNASU; 950740; -.
DR EnsemblBacteria; AAC22394; AAC22394; HI_0735.
DR KEGG; hin:HI_0735; -.
DR PATRIC; fig|71421.8.peg.769; -.
DR eggNOG; COG2908; Bacteria.
DR HOGENOM; CLU_074586_0_0_6; -.
DR OMA; FDFWFEY; -.
DR PhylomeDB; P44046; -.
DR BioCyc; HINF71421:G1GJ1-773-MON; -.
DR BRENDA; 3.6.1.54; 2529.
DR UniPathway; UPA00359; UER00480.
DR Proteomes; UP000000579; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0019897; C:extrinsic component of plasma membrane; IBA:GO_Central.
DR GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
DR GO; GO:0008758; F:UDP-2,3-diacylglucosamine hydrolase activity; IDA:UniProtKB.
DR GO; GO:0009245; P:lipid A biosynthetic process; IBA:GO_Central.
DR Gene3D; 3.60.21.10; -; 1.
DR HAMAP; MF_00575; LpxH; 1.
DR InterPro; IPR004843; Calcineurin-like_PHP_ApaH.
DR InterPro; IPR043461; LpxH-like.
DR InterPro; IPR029052; Metallo-depent_PP-like.
DR InterPro; IPR010138; UDP-diacylglucosamine_Hdrlase.
DR PANTHER; PTHR34990; PTHR34990; 1.
DR PANTHER; PTHR34990:SF1; PTHR34990:SF1; 1.
DR Pfam; PF00149; Metallophos; 1.
DR SUPFAM; SSF56300; SSF56300; 1.
DR TIGRFAMs; TIGR01854; lipid_A_lpxH; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell inner membrane; Cell membrane; Cytoplasm; Hydrolase;
KW Lipid A biosynthesis; Lipid biosynthesis; Lipid metabolism; Manganese;
KW Membrane; Metal-binding; Reference proteome.
FT CHAIN 1..237
FT /note="UDP-2,3-diacylglucosamine hydrolase"
FT /id="PRO_0000214112"
FT BINDING 9
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00575,
FT ECO:0000269|PubMed:27780190"
FT BINDING 11
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00575,
FT ECO:0000269|PubMed:27780190"
FT BINDING 42
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00575,
FT ECO:0000269|PubMed:27780190"
FT BINDING 42
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00575,
FT ECO:0000269|PubMed:27780190"
FT BINDING 80..81
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00575,
FT ECO:0000305|PubMed:27780190"
FT BINDING 80
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00575,
FT ECO:0000269|PubMed:27780190"
FT BINDING 115
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00575,
FT ECO:0000269|PubMed:27780190"
FT BINDING 123
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00575,
FT ECO:0000305|PubMed:27780190"
FT BINDING 161
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00575,
FT ECO:0000305|PubMed:27780190"
FT BINDING 165
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00575,
FT ECO:0000305|PubMed:27780190"
FT BINDING 168
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00575,
FT ECO:0000305|PubMed:27780190"
FT BINDING 196
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00575,
FT ECO:0000269|PubMed:27780190"
FT BINDING 196
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00575,
FT ECO:0000305|PubMed:27780190"
FT BINDING 198
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00575"
FT MUTAGEN 9
FT /note="D->A: 230000-fold decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:23897835"
FT MUTAGEN 11
FT /note="H->A: 17000-fold decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:23897835"
FT MUTAGEN 42
FT /note="D->A: 80000-fold decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:23897835"
FT MUTAGEN 81
FT /note="R->A: 7000-fold decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:23897835"
FT MUTAGEN 115
FT /note="H->A: 12000-fold decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:23897835"
FT MUTAGEN 117
FT /note="D->A: 2-fold decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:23897835"
FT MUTAGEN 196
FT /note="H->A: 5000-fold decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:23897835"
FT STRAND 3..7
FT /evidence="ECO:0007829|PDB:5K8K"
FT HELIX 17..29
FT /evidence="ECO:0007829|PDB:5K8K"
FT HELIX 31..33
FT /evidence="ECO:0007829|PDB:5K8K"
FT STRAND 35..41
FT /evidence="ECO:0007829|PDB:5K8K"
FT HELIX 55..69
FT /evidence="ECO:0007829|PDB:5K8K"
FT STRAND 73..77
FT /evidence="ECO:0007829|PDB:5K8K"
FT STRAND 80..82
FT /evidence="ECO:0007829|PDB:5K8K"
FT HELIX 87..93
FT /evidence="ECO:0007829|PDB:5K8K"
FT STRAND 96..98
FT /evidence="ECO:0007829|PDB:5K8K"
FT STRAND 100..106
FT /evidence="ECO:0007829|PDB:5K8K"
FT STRAND 109..114
FT /evidence="ECO:0007829|PDB:5K8K"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:5K8K"
FT HELIX 124..133
FT /evidence="ECO:0007829|PDB:5K8K"
FT HELIX 136..144
FT /evidence="ECO:0007829|PDB:5K8K"
FT HELIX 147..166
FT /evidence="ECO:0007829|PDB:5K8K"
FT HELIX 171..173
FT /evidence="ECO:0007829|PDB:5K8K"
FT HELIX 177..187
FT /evidence="ECO:0007829|PDB:5K8K"
FT STRAND 190..194
FT /evidence="ECO:0007829|PDB:5K8K"
FT STRAND 201..204
FT /evidence="ECO:0007829|PDB:5K8K"
FT STRAND 209..212
FT /evidence="ECO:0007829|PDB:5K8K"
FT STRAND 224..227
FT /evidence="ECO:0007829|PDB:5K8K"
FT STRAND 232..234
FT /evidence="ECO:0007829|PDB:5K8K"
SQ SEQUENCE 237 AA; 27786 MW; 7218733241F395B7 CRC64;
MKHSYFISDL HLSETQPELT ALFVDFMQNL APQAERLYIL GDLFDFWIGD DEQSALIQQV
KDLIKFVSDQ GVQCYFQHGN RDFLIGERFS KETGAQLLPD YQLITLYDKK ILLCHGDTLC
IDDEAYQQFR RRVHQKWLQR LFLCLPLKVR VIIAEKIRAK SNQDKQAKSQ EIMDVNQAFT
AEKVQEFGVN LLIHGHTHRE AIHQQEEFTR IVLGDWRKNY ASILKMDESG EFGFIKD
