LYM1_ARATH
ID LYM1_ARATH Reviewed; 416 AA.
AC Q93ZH0; Q5XF34; Q9SFE8;
DT 31-OCT-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=LysM domain-containing GPI-anchored protein 1;
DE Flags: Precursor;
GN Name=LYM1; OrderedLocusNames=At1g21880; ORFNames=T26F17.10, T26F17_5;
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 1).
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] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Shinn P., Chen H., Cheuk R.F., Kim C.J., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH PEPTIDOGLYCAN.
RC STRAIN=cv. Columbia;
RX PubMed=22106285; DOI=10.1073/pnas.1112862108;
RA Willmann R., Lajunen H.M., Erbs G., Newman M.-A., Kolb D., Tsuda K.,
RA Katagiri F., Fliegmann J., Bono J.-J., Cullimore J.V., Jehle A.K.,
RA Goetz F., Kulik A., Molinaro A., Lipka V., Gust A.A., Nuernberger T.;
RT "Arabidopsis lysin-motif proteins LYM1 LYM3 CERK1 mediate bacterial
RT peptidoglycan sensing and immunity to bacterial infection.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:19824-19829(2011).
CC -!- FUNCTION: Required as a cell surface receptor for peptidoglycan (PGN)
CC elicitor signaling leading to innate immunity. Plays an essential role
CC in detecting PGNs and restricting bacterial growth (of Pseudomonas
CC syringae pv. tomato DC3000 for example). {ECO:0000269|PubMed:22106285}.
CC -!- SUBUNIT: Interacts with peptidoglycans. {ECO:0000269|PubMed:22106285}.
CC -!- SUBCELLULAR LOCATION: [Isoform 1]: Cell membrane; Lipid-anchor, GPI-
CC anchor.
CC -!- SUBCELLULAR LOCATION: [Isoform 2]: Secreted {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q93ZH0-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q93ZH0-2; Sequence=VSP_008744;
CC -!- DISRUPTION PHENOTYPE: Impaired sensitivity to peptidoglycans (PGNs)
CC leading to higher susceptibility to infection with virulent Pseudomonas
CC syringae pv. tomato DC3000. {ECO:0000269|PubMed:22106285}.
CC -!- MISCELLANEOUS: [Isoform 1]: GPI-anchored form.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing donor splice
CC site. Has no GPI-anchor. {ECO:0000305}.
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DR EMBL; AC013482; AAF16531.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE30167.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE30168.1; -; Genomic_DNA.
DR EMBL; AY057542; AAL09782.1; -; mRNA.
DR EMBL; BT015782; AAU90072.1; -; mRNA.
DR PIR; B86352; B86352.
DR RefSeq; NP_564153.1; NM_102036.4. [Q93ZH0-1]
DR RefSeq; NP_849697.1; NM_179366.1. [Q93ZH0-2]
DR AlphaFoldDB; Q93ZH0; -.
DR SMR; Q93ZH0; -.
DR STRING; 3702.AT1G21880.2; -.
DR iPTMnet; Q93ZH0; -.
DR PaxDb; Q93ZH0; -.
DR PRIDE; Q93ZH0; -.
DR ProteomicsDB; 238747; -. [Q93ZH0-1]
DR EnsemblPlants; AT1G21880.1; AT1G21880.1; AT1G21880. [Q93ZH0-2]
DR EnsemblPlants; AT1G21880.2; AT1G21880.2; AT1G21880. [Q93ZH0-1]
DR GeneID; 838790; -.
DR Gramene; AT1G21880.1; AT1G21880.1; AT1G21880. [Q93ZH0-2]
DR Gramene; AT1G21880.2; AT1G21880.2; AT1G21880. [Q93ZH0-1]
DR KEGG; ath:AT1G21880; -.
DR Araport; AT1G21880; -.
DR TAIR; locus:2201143; AT1G21880.
DR eggNOG; ENOG502QWAT; Eukaryota.
DR InParanoid; Q93ZH0; -.
DR OMA; VKFMMAI; -.
DR PhylomeDB; Q93ZH0; -.
DR PRO; PR:Q93ZH0; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q93ZH0; baseline and differential.
DR Genevisible; Q93ZH0; AT.
DR GO; GO:0031225; C:anchored component of membrane; TAS:TAIR.
DR GO; GO:0046658; C:anchored component of plasma membrane; IDA:TAIR.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; HDA:TAIR.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0042834; F:peptidoglycan binding; IDA:TAIR.
DR GO; GO:0006952; P:defense response; IEA:UniProtKB-KW.
DR GO; GO:0006955; P:immune response; IMP:TAIR.
DR CDD; cd00118; LysM; 2.
DR Gene3D; 3.10.350.10; -; 2.
DR InterPro; IPR018392; LysM_dom.
DR InterPro; IPR036779; LysM_dom_sf.
DR Pfam; PF01476; LysM; 2.
DR SMART; SM00257; LysM; 2.
DR SUPFAM; SSF54106; SSF54106; 1.
DR PROSITE; PS51782; LYSM; 2.
PE 1: Evidence at protein level;
KW Alternative splicing; Cell membrane; Disulfide bond; Glycoprotein;
KW GPI-anchor; Lipoprotein; Membrane; Plant defense; Reference proteome;
KW Repeat; Secreted; Signal.
FT SIGNAL 1..27
FT /evidence="ECO:0000255"
FT CHAIN 28..391
FT /note="LysM domain-containing GPI-anchored protein 1"
FT /id="PRO_0000021627"
FT PROPEP 392..416
FT /note="Removed in mature form"
FT /evidence="ECO:0000255"
FT /id="PRO_0000021628"
FT DOMAIN 110..157
FT /note="LysM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01118"
FT DOMAIN 176..219
FT /note="LysM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01118"
FT REGION 356..376
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT LIPID 391
FT /note="GPI-anchor amidated alanine"
FT /evidence="ECO:0000255"
FT CARBOHYD 37
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 165
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 241
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 288
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 299
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 310
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT DISULFID 34..100
FT /evidence="ECO:0000250|UniProtKB:Q8H8C7"
FT DISULFID 40..163
FT /evidence="ECO:0000250|UniProtKB:Q8H8C7"
FT DISULFID 98..161
FT /evidence="ECO:0000250|UniProtKB:Q8H8C7"
FT DISULFID 100..163
FT /evidence="ECO:0000250|UniProtKB:Q8H8C7"
FT DISULFID 224..256
FT /evidence="ECO:0000250|UniProtKB:Q8H8C7"
FT DISULFID 251..279
FT /evidence="ECO:0000250|UniProtKB:Q8H8C7"
FT VAR_SEQ 317..416
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_008744"
SQ SEQUENCE 416 AA; 43490 MW; 2655D586032D019E CRC64;
MKIPEKPIFL IFVSLILASS LTFTATAKST IEPCSSNDTC NALLGYTLYT DLKVSEVASL
FQVDPISILL ANAIDISYPD VENHILPSKL FLKIPITCSC VDGIRKSVST HYKTRPSDNL
GSIADSVYGG LVSAEQIQEA NSVNDPSLLD VGTSLVIPLP CACFNGTDNS LPAVYLSYVV
KEIDTLVGIA RRYSTTITDL MNVNAMGAPD VSSGDILAVP LSACASKFPR YASDFGLIVP
NGSYALAAGH CVQCSCALGS RNLYCEPASL AVSCSSMQCR NSNLMLGNIT VQQTSAGCNV
TTCDYNGIAN GTILTMLTRS LQPRCPGPQQ FAPLLAPPDT VPRDVMYAPA PSPDFDGPGS
IASSPRSSML PGGGILPGNP ANGPAGSIST ASASSVSYFF ITFLISIASF SLALSS
