LPXC1_ARATH
ID LPXC1_ARATH Reviewed; 326 AA.
AC F4IAT8; B3H6R1; F4IAW2; P0C2G7; Q56X64; Q56XG5; Q7GAV1; Q8GXP0; Q8LPR6;
AC Q9FE36; Q9FXK3; Q9FXK7;
DT 03-OCT-2012, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2012, sequence version 2.
DT 03-AUG-2022, entry version 90.
DE RecName: Full=Probable UDP-3-O-acyl-N-acetylglucosamine deacetylase 1, mitochondrial {ECO:0000250|UniProtKB:P0A725};
DE Short=UDP-3-O-acyl-GlcNAc deacetylase 1 {ECO:0000250|UniProtKB:P0A725};
DE EC=3.5.1.108 {ECO:0000250|UniProtKB:P0A725};
DE AltName: Full=Protein LIPID X C1;
DE Short=AtLpxC1;
DE AltName: Full=UDP-3-O-[R-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase 1 {ECO:0000250|UniProtKB:P0A725};
DE Flags: Precursor;
GN Name=LPXC1; OrderedLocusNames=At1g24793; ORFNames=F5A9.18;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP PATHWAY, SUBCELLULAR LOCATION, GENE FAMILY, AND NOMENCLATURE.
RX PubMed=21709257; DOI=10.1073/pnas.1108840108;
RA Li C., Guan Z., Liu D., Raetz C.R.;
RT "Pathway for lipid A biosynthesis in Arabidopsis thaliana resembling that
RT of Escherichia coli.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:11387-11392(2011).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND CLEAVAGE OF TRANSIT PEPTIDE AFTER
RP TYR-21.
RX PubMed=25732537; DOI=10.1093/jxb/erv064;
RA Carrie C., Venne A.S., Zahedi R.P., Soll J.;
RT "Identification of cleavage sites and substrate proteins for two
RT mitochondrial intermediate peptidases in Arabidopsis thaliana.";
RL J. Exp. Bot. 66:2691-2708(2015).
CC -!- FUNCTION: Involved in the biosynthesis of lipid A, a phosphorylated
CC glycolipid that in bacteria anchors the lipopolysaccharide to the outer
CC membrane of the cell. Lipid A-like molecules in plants may serve as
CC structural components of the outer membranes of mitochondria and/or
CC chloroplasts, or may be involved in signal transduction or plant
CC defense responses (Potential). {ECO:0000305}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine +
CC H2O = a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + acetate;
CC Xref=Rhea:RHEA:67816, ChEBI:CHEBI:15377, ChEBI:CHEBI:30089,
CC ChEBI:CHEBI:137740, ChEBI:CHEBI:173225; EC=3.5.1.108;
CC Evidence={ECO:0000250|UniProtKB:P0A725};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:P0A725};
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 2/6. {ECO:0000269|PubMed:21709257}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:21709257,
CC ECO:0000305|PubMed:25732537}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=F4IAT8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=F4IAT8-2; Sequence=VSP_022944, VSP_022945;
CC Name=3;
CC IsoId=F4IAT8-3; Sequence=VSP_034100;
CC -!- MISCELLANEOUS: Plants silencing LPXC do not have altered morphology
CC compared to wild-type plants when grown under normal growth conditions,
CC but they do not accumulate 2,3-diacylglucosamine-1-phosphate.
CC {ECO:0000305|PubMed:21709257}.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing donor splice
CC site. {ECO:0000305}.
CC -!- MISCELLANEOUS: [Isoform 3]: May be due to intron retention.
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the LpxC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAG03124.1; Type=Erroneous gene model prediction; Note=The predicted gene has been split into 2 genes: At1g24793 and At1g24800.; Evidence={ECO:0000305};
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DR EMBL; AC004133; AAG03124.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE30562.1; -; Genomic_DNA.
DR EMBL; AY094436; AAM19808.1; -; mRNA.
DR EMBL; AK221709; BAD95433.1; -; mRNA.
DR EMBL; AK221813; BAD94001.1; -; mRNA.
DR RefSeq; NP_001117349.4; NM_001123877.5. [F4IAT8-1]
DR RefSeq; NP_001185090.1; NM_001198161.1. [F4IAT8-1]
DR RefSeq; NP_173874.2; NM_102312.3. [F4IAT8-1]
DR RefSeq; NP_849706.4; NM_179375.4. [F4IAT8-1]
DR AlphaFoldDB; F4IAT8; -.
DR SMR; F4IAT8; -.
DR STRING; 3702.AT1G24793.1; -.
DR PaxDb; F4IAT8; -.
DR EnsemblPlants; AT1G24793.1; AT1G24793.1; AT1G24793.
DR EnsemblPlants; AT1G25054.1; AT1G25054.1; AT1G25054.
DR EnsemblPlants; AT1G25145.1; AT1G25145.1; AT1G25145.
DR EnsemblPlants; AT1G25210.2; AT1G25210.2; AT1G25210.
DR GeneID; 10723064; -.
DR GeneID; 839084; -.
DR GeneID; 839094; -.
DR GeneID; 839102; -.
DR Gramene; AT1G24793.1; AT1G24793.1; AT1G24793.
DR Gramene; AT1G25054.1; AT1G25054.1; AT1G25054.
DR Gramene; AT1G25145.1; AT1G25145.1; AT1G25145.
DR Gramene; AT1G25210.2; AT1G25210.2; AT1G25210.
DR KEGG; ath:AT1G24793; -.
DR KEGG; ath:AT1G25054; -.
DR KEGG; ath:AT1G25145; -.
DR KEGG; ath:AT1G25210; -.
DR Araport; AT1G24793; -.
DR eggNOG; ENOG502QT9Y; Eukaryota.
DR HOGENOM; CLU_046528_0_0_1; -.
DR OMA; IVFYRSD; -.
DR PhylomeDB; F4IAT8; -.
DR UniPathway; UPA00359; UER00478.
DR PRO; PR:F4IAT8; -.
DR Proteomes; UP000006548; Chromosome 1.
DR GO; GO:0005739; C:mitochondrion; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008759; F:UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity; IMP:UniProtKB.
DR GO; GO:0103117; F:UDP-3-O-acyl-N-acetylglucosamine deacetylase activity; IEA:UniProtKB-EC.
DR GO; GO:0009245; P:lipid A biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:2001289; P:lipid X metabolic process; IMP:UniProtKB.
DR Gene3D; 3.30.1700.10; -; 1.
DR Gene3D; 3.30.230.20; -; 1.
DR HAMAP; MF_00388; LpxC; 1.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR InterPro; IPR004463; UDP-acyl_GlcNac_deAcase.
DR InterPro; IPR011334; UDP-acyl_GlcNac_deAcase_C.
DR InterPro; IPR015870; UDP-acyl_N-AcGlcN_deAcase_N.
DR PANTHER; PTHR33694; PTHR33694; 1.
DR Pfam; PF03331; LpxC; 1.
DR SUPFAM; SSF54211; SSF54211; 2.
DR TIGRFAMs; TIGR00325; lpxC; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Hydrolase; Lipid A biosynthesis; Lipid biosynthesis;
KW Lipid metabolism; Metal-binding; Mitochondrion; Reference proteome;
KW Transit peptide; Zinc.
FT TRANSIT 1..21
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:25732537"
FT CHAIN 22..326
FT /note="Probable UDP-3-O-acyl-N-acetylglucosamine
FT deacetylase 1, mitochondrial"
FT /id="PRO_0000274929"
FT BINDING 109
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:P0A725"
FT BINDING 281
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:P0A725"
FT BINDING 285
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:P0A725"
FT VAR_SEQ 1..170
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|Ref.4"
FT /id="VSP_034100"
FT VAR_SEQ 261..265
FT /note="CSAEH -> SLSMD (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_022944"
FT VAR_SEQ 267..326
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_022945"
FT CONFLICT 84
FT /note="S -> P (in Ref. 3; BAD94001)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 326 AA; 35717 MW; CBF391A5DFB4EEA9 CRC64;
MRLPVTVKAT KPSFLVIWIR YSSAASSPTV SLNPSGRLQQ TLAGSVEVKG KSLHSGKFST
VKLNPEIAGA GRFFEFRSRF IPASIEFAQE SPLCTTLLKD ELKIRTVEHL LSALEAKGVD
NCRIQIESES SDDREVEVPI FDGSAKEWVD AIQGVGINAA QNHDGESVEK MVAHVNKPVY
VCKNDTFVAA FPALETRITC GIDFPQVPAI GCQWFSWRPI HESSFAKDIA SSRTFCVYEE
VERMREAGLI KGGSLDNAIV CSAEHGWMNP PLRFDDEACR HKILDLIGDL SLVSRGGNGG
LPVAHIVAYK AGHALHTDLA RHLTMD
