LRP1_ARATH
ID LRP1_ARATH Reviewed; 320 AA.
AC Q94CK9; F4K0X0; Q38848; Q3E9I3;
DT 11-DEC-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=Protein LATERAL ROOT PRIMORDIUM 1;
GN Name=LRP1; OrderedLocusNames=At5g12330; ORFNames=T2L20;
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 [GENOMIC DNA] (ISOFORM 1), TISSUE SPECIFICITY, AND
RP DEVELOPMENTAL STAGE.
RC STRAIN=cv. No-0;
RX PubMed=7647564; DOI=10.2307/3870175;
RA Smith D.L., Fedoroff N.V.;
RT "LRP1, a gene expressed in lateral and adventitious root primordia of
RT arabidopsis.";
RL Plant Cell 7:735-745(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Cheuk R.F., Chen H., Kim C.J., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (FEB-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, DISRUPTION PHENOTYPE, SUBUNIT, GENE FAMILY, AND NOMENCLATURE.
RX PubMed=16740146; DOI=10.1111/j.1365-313x.2006.02774.x;
RA Kuusk S., Sohlberg J.J., Magnus Eklund D., Sundberg E.;
RT "Functionally redundant SHI family genes regulate Arabidopsis gynoecium
RT development in a dose-dependent manner.";
RL Plant J. 47:99-111(2006).
RN [6]
RP FUNCTION, AND REPRESSION BY LDL1.
RX PubMed=18835563; DOI=10.1016/j.jmb.2008.09.040;
RA Krichevsky A., Zaltsman A., Kozlovsky S.V., Tian G.-W., Citovsky V.;
RT "Regulation of root elongation by histone acetylation in Arabidopsis.";
RL J. Mol. Biol. 385:45-50(2009).
RN [7]
RP GENE FAMILY.
RX PubMed=21976484; DOI=10.1104/pp.111.182253;
RA Eklund D.M., Cierlik I., Staaldal V., Claes A.R., Vestman D., Chandler J.,
RA Sundberg E.;
RT "Expression of Arabidopsis SHORT INTERNODES/STYLISH family genes in auxin
RT biosynthesis zones of aerial organs is dependent on a GCC box-like
RT regulatory element.";
RL Plant Physiol. 157:2069-2080(2011).
CC -!- FUNCTION: Transcription activator that binds DNA on 5'-ACTCTAC-3' and
CC promotes auxin homeostasis-regulating gene expression (e.g. YUC genes),
CC as well as genes affecting stamen development, cell expansion and
CC timing of flowering. Synergistically with other SHI-related proteins,
CC regulates gynoecium, stamen and leaf development in a dose-dependent
CC manner, controlling apical-basal patterning. Promotes style and stigma
CC formation, and influence vascular development during gynoecium
CC development. May also have a role in the formation and/or maintenance
CC of the shoot apical meristem (SAM). Modulates root growth.
CC {ECO:0000269|PubMed:16740146, ECO:0000269|PubMed:18835563}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16740146}.
CC -!- INTERACTION:
CC Q94CK9-3; Q9SI19: SRS4; NbExp=5; IntAct=EBI-15199884, EBI-15193733;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q94CK9-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q94CK9-2; Sequence=VSP_053449;
CC Name=3;
CC IsoId=Q94CK9-3; Sequence=VSP_053448;
CC -!- TISSUE SPECIFICITY: Restricted to lateral root primordia.
CC {ECO:0000269|PubMed:7647564}.
CC -!- DEVELOPMENTAL STAGE: Expressed during the early stages of root
CC primordium development and disappears prior to the emergence of lateral
CC roots from the parent root. {ECO:0000269|PubMed:7647564}.
CC -!- INDUCTION: Expression repressed by LDL1 via histone H3 and H4
CC deacetylation. {ECO:0000269|PubMed:18835563}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype.
CC {ECO:0000269|PubMed:16740146}.
CC -!- SIMILARITY: Belongs to the SHI protein family. {ECO:0000305}.
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DR EMBL; U24702; AAA87790.1; -; Genomic_DNA.
DR EMBL; AL592312; CAC42894.1; -; Genomic_DNA.
DR EMBL; CP002688; AED91793.1; -; Genomic_DNA.
DR EMBL; CP002688; AED91794.1; -; Genomic_DNA.
DR EMBL; CP002688; AED91795.1; -; Genomic_DNA.
DR EMBL; CP002688; AED91796.1; -; Genomic_DNA.
DR EMBL; BT020614; AAW81722.1; -; mRNA.
DR RefSeq; NP_001190295.1; NM_001203366.1. [Q94CK9-3]
DR RefSeq; NP_568266.1; NM_121271.4. [Q94CK9-1]
DR RefSeq; NP_974771.1; NM_203042.1. [Q94CK9-1]
DR RefSeq; NP_974772.1; NM_203043.2. [Q94CK9-2]
DR AlphaFoldDB; Q94CK9; -.
DR BioGRID; 16386; 15.
DR IntAct; Q94CK9; 12.
DR STRING; 3702.AT5G12330.4; -.
DR iPTMnet; Q94CK9; -.
DR PaxDb; Q94CK9; -.
DR PRIDE; Q94CK9; -.
DR ProteomicsDB; 238614; -. [Q94CK9-1]
DR EnsemblPlants; AT5G12330.1; AT5G12330.1; AT5G12330. [Q94CK9-1]
DR EnsemblPlants; AT5G12330.2; AT5G12330.2; AT5G12330. [Q94CK9-1]
DR EnsemblPlants; AT5G12330.3; AT5G12330.3; AT5G12330. [Q94CK9-2]
DR EnsemblPlants; AT5G12330.4; AT5G12330.4; AT5G12330. [Q94CK9-3]
DR GeneID; 831108; -.
DR Gramene; AT5G12330.1; AT5G12330.1; AT5G12330. [Q94CK9-1]
DR Gramene; AT5G12330.2; AT5G12330.2; AT5G12330. [Q94CK9-1]
DR Gramene; AT5G12330.3; AT5G12330.3; AT5G12330. [Q94CK9-2]
DR Gramene; AT5G12330.4; AT5G12330.4; AT5G12330. [Q94CK9-3]
DR KEGG; ath:AT5G12330; -.
DR Araport; AT5G12330; -.
DR TAIR; locus:505006601; AT5G12330.
DR eggNOG; ENOG502QU6D; Eukaryota.
DR HOGENOM; CLU_041493_0_0_1; -.
DR OrthoDB; 1262400at2759; -.
DR PhylomeDB; Q94CK9; -.
DR PRO; PR:Q94CK9; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q94CK9; baseline and differential.
DR Genevisible; Q94CK9; AT.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0048653; P:anther development; IGI:TAIR.
DR GO; GO:0009851; P:auxin biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0009734; P:auxin-activated signaling pathway; IEA:UniProtKB-KW.
DR GO; GO:0009555; P:pollen development; IGI:TAIR.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IBA:GO_Central.
DR GO; GO:0009733; P:response to auxin; IEP:TAIR.
DR GO; GO:0048364; P:root development; IMP:TAIR.
DR InterPro; IPR007818; SHI.
DR InterPro; IPR006511; SHI_C.
DR InterPro; IPR006510; Znf_LRP1.
DR PANTHER; PTHR31604; PTHR31604; 1.
DR TIGRFAMs; TIGR01624; LRP1_Cterm; 1.
DR TIGRFAMs; TIGR01623; put_zinc_LRP1; 1.
PE 1: Evidence at protein level;
KW Activator; Alternative splicing; Auxin biosynthesis;
KW Auxin signaling pathway; Developmental protein; DNA-binding; Metal-binding;
KW Nucleus; Reference proteome; Zinc.
FT CHAIN 1..320
FT /note="Protein LATERAL ROOT PRIMORDIUM 1"
FT /id="PRO_0000424582"
FT DNA_BIND 112..139
FT /note="Zn(2)-C6 fungal-type; degenerate"
FT /evidence="ECO:0000250"
FT REGION 90..110
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 150..223
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 256..259
FT /note="Required for homo- and heterodimerization"
FT /evidence="ECO:0000250"
FT COMPBIAS 162..217
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 112
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 112
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 115
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 123
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 128
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 128
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 132
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 139
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT VAR_SEQ 1
FT /note="M -> MYIGALCSVATTRRHNLPTSDSGAFTDWAATTTTPSRATEDLSLGFN
FT AGSSVIHGGLGSASVAAGVPSWPPGSSVRYGLPSSAAATEM (in isoform 3)"
FT /evidence="ECO:0000305"
FT /id="VSP_053448"
FT VAR_SEQ 215..320
FT /note="DGGGSREAWPGQVRAAAVFKCVRVTAVEDGDDEYAYQAVVKIGGHVFKGFLY
FT DQGLEPKEGFPSMSDLHLGGSANNHNGVSASAPILDPPNVVYGGGGGSGGGFYS -> G
FT SFTFSLVYIAT (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_053449"
FT CONFLICT 52
FT /note="T -> P (in Ref. 1; AAA87790)"
FT /evidence="ECO:0000305"
FT CONFLICT 298
FT /note="A -> V (in Ref. 1; AAA87790)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 320 AA; 33618 MW; 09F30160B6E35AB9 CRC64;
MGMVGLRDVF LVAPAYHHQN AGVISGSDHM NSNAAAAAAL GVGVIPLLTA GTPQQNVEDS
DINFLGNNRR WQNNNNNHET QYLHFKSTNQ TTVGTSSNNS GSGSGASGTA TCQDCGNQAK
KECKQRRCRT CCKSRGFDCS THVKSTWVSA ARRRERQVMP TGANPTAGSS LSTSSGTKKP
RIVGSQQQQQ QQATSHTSTS NTPPQSFETS SSRQDGGGSR EAWPGQVRAA AVFKCVRVTA
VEDGDDEYAY QAVVKIGGHV FKGFLYDQGL EPKEGFPSMS DLHLGGSANN HNGVSASAPI
LDPPNVVYGG GGGSGGGFYS
