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LPXH_XYLFM
ID   LPXH_XYLFM              Reviewed;         250 AA.
AC   B0U5J4;
DT   14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT   08-APR-2008, sequence version 1.
DT   03-AUG-2022, entry version 85.
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};
DE   AltName: Full=UDP-2,3-diacylglucosamine diphosphatase {ECO:0000255|HAMAP-Rule:MF_00575};
GN   Name=lpxH {ECO:0000255|HAMAP-Rule:MF_00575};
GN   OrderedLocusNames=Xfasm12_2158;
OS   Xylella fastidiosa (strain M12).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;
OC   Xanthomonadaceae; Xylella.
OX   NCBI_TaxID=405440;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=M12;
RX   PubMed=20601474; DOI=10.1128/jb.00651-10;
RA   Chen J., Xie G., Han S., Chertkov O., Sims D., Civerolo E.L.;
RT   "Whole genome sequences of two Xylella fastidiosa strains (M12 and M23)
RT   causing almond leaf scorch disease in California.";
RL   J. Bacteriol. 192:4534-4534(2010).
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}.
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   -!- COFACTOR:
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00575};
CC       Note=Binds 2 Mn(2+) ions per subunit in a binuclear metal center.
CC       {ECO:0000255|HAMAP-Rule:MF_00575};
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-
CC       Rule:MF_00575}.
CC   -!- SUBCELLULAR LOCATION: Cell inner membrane {ECO:0000255|HAMAP-
CC       Rule:MF_00575}; Peripheral membrane protein {ECO:0000255|HAMAP-
CC       Rule:MF_00575}; Cytoplasmic side {ECO:0000255|HAMAP-Rule:MF_00575}.
CC   -!- SIMILARITY: Belongs to the LpxH family. {ECO:0000255|HAMAP-
CC       Rule:MF_00575}.
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DR   EMBL; CP000941; ACA13012.1; -; Genomic_DNA.
DR   RefSeq; WP_012338111.1; NC_010513.1.
DR   AlphaFoldDB; B0U5J4; -.
DR   SMR; B0U5J4; -.
DR   KEGG; xfm:Xfasm12_2158; -.
DR   HOGENOM; CLU_074586_0_0_6; -.
DR   OMA; FDFWFEY; -.
DR   OrthoDB; 1690667at2; -.
DR   UniPathway; UPA00359; UER00480.
DR   GO; GO:0005737; C:cytoplasm; IEA:InterPro.
DR   GO; GO:0019897; C:extrinsic component of plasma membrane; IEA:UniProtKB-UniRule.
DR   GO; GO:0030145; F:manganese ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0008758; F:UDP-2,3-diacylglucosamine hydrolase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0009245; P:lipid A biosynthetic process; IEA:UniProtKB-UniRule.
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   3: Inferred from homology;
KW   Cell inner membrane; Cell membrane; Hydrolase; Lipid A biosynthesis;
KW   Lipid biosynthesis; Lipid metabolism; Manganese; Membrane; Metal-binding.
FT   CHAIN           1..250
FT                   /note="UDP-2,3-diacylglucosamine hydrolase"
FT                   /id="PRO_1000129546"
FT   BINDING         8
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00575"
FT   BINDING         10
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00575"
FT   BINDING         41
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00575"
FT   BINDING         41
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00575"
FT   BINDING         79..80
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00575"
FT   BINDING         79
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00575"
FT   BINDING         114
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00575"
FT   BINDING         122
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00575"
FT   BINDING         160
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00575"
FT   BINDING         172
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00575"
FT   BINDING         175
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00575"
FT   BINDING         203
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00575"
FT   BINDING         203
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00575"
FT   BINDING         205
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00575"
SQ   SEQUENCE   250 AA;  27587 MW;  ACE9967C631DD4E9 CRC64;
     MTTLIISDLH LDPLRPVVTE LFLRFLREQV SGADALYILG DLFEVWIGDD MPSEVADMVA
     AALRTYADAG TPLYFMPGNR DFLVGADYAA RAGFRILPDP CVVDLYGEPT LLLHGDLLCT
     DDIAYQAFRA QTRDPEFIAQ FLTQTLSARL AFSQQARLAS HAHQSGLKQE NDSTQFEKIT
     DVVPADVAAM FACYGVNRMI HGHTHRPALH MLQVAECACT RVVLGDWYQQ GSVLCVDADG
     LVLEQLLLPG
 
 
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