HAMAP rule MF_00575

General rule information [?]

Accession	MF_00575
Dates	31-JUL-2002 (Created) 17-FEB-2023 (Last updated, Version 30)

Name

LpxH

Scope

Bacteria; Pseudomonadota

Templates

P43341 (LPXH_ECOLI); P44046 (LPXH_HAEIN); Q9I2V0 (LPXH_PSEAE): [Recover all]

Triggered by

HAMAP; MF_00575 (Get profile general information and statistics)

Propagated annotation [?]

Identifier, protein and gene names [?]

Identifier

LPXH

Protein name

RecName:		Full=UDP-2,3-diacylglucosamine hydrolase;
		EC 3.6.1.54;
AltName:		Full=UDP-2,3-diacylglucosamine diphosphatase;

Gene name

lpxH

Comments [?]

Function	Hydrolyzes the pyrophosphate bond of UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP by catalyzing the attack of water at the alpha-P atom. Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell.
Catalytic activity	RHEA:25213: H2O + UDP-2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosamine = 2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl 1-phosphate + 2 H(+) + UMP EC 3.6.1.54
Cofactor	Mn(2+) Note: Binds 2 Mn(2+) ions per subunit in a binuclear metal center
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 4/6.
Subcellular location	Cell inner membrane; Peripheral membrane protein; Cytoplasmic side.
Similarity	Belongs to the LpxH family.

Keywords [?]

Cell inner membrane
Cell membrane
Hydrolase
Lipid A biosynthesis
Lipid biosynthesis
Lipid metabolism
Manganese
Membrane
Metal-binding

Gene Ontology [?]

GO:0008758; Molecular function: UDP-2,3-diacylglucosamine hydrolase activity.
GO:0030145; Molecular function: manganese ion binding.
GO:0009245; Biological process: lipid A biosynthetic process.
GO:0019897; Cellular component: extrinsic component of plasma membrane.

Cross-references [?]

Pfam	PF00149; Metallophos; 1;
	PF12850; Metallophos_2; 1;
TIGRFAMs	TIGR01854; Lipid_A_lpxH; 1;

Features [?]

From: LPXH_PSEAE (Q9I2V0)

Key From To Description Tag Condition FTGroup

BINDING 79 80 /ligand="substrate N-[RH]

BINDING 8 8 /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="1 D

BINDING 10 10 /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="1 H

BINDING 41 41 /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="1 D

BINDING 41 41 /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="2 D

BINDING 79 79 /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="2 N

BINDING 114 114 /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="2 H

BINDING 195 195 /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="2 H

BINDING 197 197 /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="1 H

BINDING 122 122 /ligand="substrate D

BINDING (Optional) 160 160 /ligand="substrate S

BINDING (Optional) 164 164 /ligand="substrate [TKNQED]

BINDING (Optional) 167 167 /ligand="substrate [KRQN]

BINDING 195 195 /ligand="substrate H

Additional information [?]

Size range	234-268 amino acids
Related rules	None
Fusion	None
Comments	This step in lipid A biosynthesis is carried out by LpxH in beta- and gammaproteobacteria, by LpxI in alphaproteobacteria, and by LpxG in Chlamydiota. LpxH and LpxG are unique members of the metal-dependent calcineurin-like phosphoesterase (CLP) family, although they share limited sequence similarity. LpxI, on the other hand, is structurally and mechanistically unrelated to LpxH and LpxG. LpxI uses water to attack the beta-phosphate, whereas LpxH and LpxG use water to attack the alpha-phosphate on the common UDP-DAGn substrate. Among these three enzymes, LpxH is most widespread, functioning in ~70% of Gram-negative bacteria and the vast majority of Gram-negative pathogens. (from PubMed:27780190) Possible wrong start in RALSO

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