ICLR_ECOLI
ID ICLR_ECOLI Reviewed; 274 AA.
AC P16528; P76782; Q2M6T6;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1990, sequence version 1.
DT 03-AUG-2022, entry version 189.
DE RecName: Full=Transcriptional repressor IclR {ECO:0000305};
DE Short=Acetate operon repressor;
GN Name=iclR; OrderedLocusNames=b4018, JW3978;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2185227; DOI=10.1128/jb.172.5.2642-2649.1990;
RA Sunnarborg A., Klumpp D.J., Chung T., Laporte D.C.;
RT "Regulation of the glyoxylate bypass operon: cloning and characterization
RT of iclR.";
RL J. Bacteriol. 172:2642-2649(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1995431; DOI=10.1016/0378-1119(91)90006-w;
RA Negre D., Cortay J.-C., Old I.G., Galinier A., Richaud C., Saint-Girons I.,
RA Cozzone A.J.;
RT "Overproduction and characterization of the iclR gene product of
RT Escherichia coli K-12 and comparison with that of Salmonella typhimurium
RT LT2.";
RL Gene 97:29-37(1991).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8265357; DOI=10.1093/nar/21.23.5408;
RA Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.;
RT "Analysis of the Escherichia coli genome. IV. DNA sequence of the region
RT from 89.2 to 92.8 minutes.";
RL Nucleic Acids Res. 21:5408-5417(1993).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 262-274.
RX PubMed=1995429; DOI=10.1016/0378-1119(91)90024-6;
RA Galinier A., Bleicher F., Negre D., Perriere G., Duclos B., Cozzone A.J.,
RA Cortay J.-C.;
RT "Primary structure of the intergenic region between aceK and iclR in the
RT Escherichia coli chromosome.";
RL Gene 97:149-150(1991).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 98-274 IN COMPLEXES WITH PYRUVATE
RP AND GLYOXYLATE, SUBUNIT, AND MUTAGENESIS OF LEU-143; MET-146; LEU-154 AND
RP LEU-220.
RX PubMed=17426033; DOI=10.1074/jbc.m610838200;
RA Lorca G.L., Ezersky A., Lunin V.V., Walker J.R., Altamentova S.,
RA Evdokimova E., Vedadi M., Bochkarev A., Savchenko A.;
RT "Glyoxylate and pyruvate are antagonistic effectors of the Escherichia coli
RT IclR transcriptional regulator.";
RL J. Biol. Chem. 282:16476-16491(2007).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 98-274.
RA Walker J.R., Skarina T., Kudrytska M., Arrowsmith C., Edwards A.,
RA Savchenko A.;
RT "Crystal structure analysis of the E. coli glyoxylate regulatory protein
RT ligand binding domain.";
RL Submitted (JAN-2005) to the PDB data bank.
CC -!- FUNCTION: Regulation of the glyoxylate bypass operon (aceBAK), which
CC encodes isocitrate lyase, malate synthase as well as isocitrate
CC dehydrogenase kinase/phosphorylase. Glyoxylate disrupts the interaction
CC with the promoter by favoring the inactive dimeric form. Pyruvate
CC enhances promoter binding by stabilizing the tetrameric form.
CC -!- SUBUNIT: Homotetramer and homodimer. Homotetramer in its active, DNA-
CC bound form. Homodimer in its inactive form.
CC {ECO:0000269|PubMed:17426033}.
CC -!- INTERACTION:
CC P16528; P67910: hldD; NbExp=2; IntAct=EBI-552904, EBI-543760;
CC -!- MISCELLANEOUS: Glyoxylate and pyruvate occupy the same site.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA50561.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAC43112.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; M31761; AAA24008.1; -; Genomic_DNA.
DR EMBL; M63914; AAA50561.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00006; AAC43112.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC76988.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE78020.1; -; Genomic_DNA.
DR EMBL; M63497; AAA73003.1; -; Genomic_DNA.
DR RefSeq; NP_418442.2; NC_000913.3.
DR RefSeq; WP_000226403.1; NZ_STEB01000022.1.
DR PDB; 1TD5; X-ray; 2.30 A; A/B/C/D=98-274.
DR PDB; 2O99; X-ray; 1.70 A; A/B/C/D=98-274.
DR PDB; 2O9A; X-ray; 1.80 A; A/B/C/D=98-274.
DR PDBsum; 1TD5; -.
DR PDBsum; 2O99; -.
DR PDBsum; 2O9A; -.
DR AlphaFoldDB; P16528; -.
DR SMR; P16528; -.
DR BioGRID; 4263460; 10.
DR DIP; DIP-10008N; -.
DR IntAct; P16528; 17.
DR MINT; P16528; -.
DR STRING; 511145.b4018; -.
DR PaxDb; P16528; -.
DR PRIDE; P16528; -.
DR EnsemblBacteria; AAC76988; AAC76988; b4018.
DR EnsemblBacteria; BAE78020; BAE78020; BAE78020.
DR GeneID; 67414670; -.
DR GeneID; 948524; -.
DR KEGG; ecj:JW3978; -.
DR KEGG; eco:b4018; -.
DR PATRIC; fig|1411691.4.peg.2695; -.
DR EchoBASE; EB0486; -.
DR eggNOG; COG1414; Bacteria.
DR HOGENOM; CLU_062618_7_1_6; -.
DR InParanoid; P16528; -.
DR OMA; EPDRLHR; -.
DR PhylomeDB; P16528; -.
DR BioCyc; EcoCyc:PD04099; -.
DR EvolutionaryTrace; P16528; -.
DR PRO; PR:P16528; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IBA:GO_Central.
DR GO; GO:0006097; P:glyoxylate cycle; IEA:UniProtKB-KW.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IBA:GO_Central.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IMP:EcoCyc.
DR Gene3D; 1.10.10.10; -; 1.
DR Gene3D; 3.30.450.40; -; 1.
DR InterPro; IPR029016; GAF-like_dom_sf.
DR InterPro; IPR014757; Tscrpt_reg_IclR_C.
DR InterPro; IPR005471; Tscrpt_reg_IclR_N.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR InterPro; IPR036390; WH_DNA-bd_sf.
DR Pfam; PF09339; HTH_IclR; 1.
DR Pfam; PF01614; IclR; 1.
DR SMART; SM00346; HTH_ICLR; 1.
DR SUPFAM; SSF46785; SSF46785; 1.
DR PROSITE; PS51077; HTH_ICLR; 1.
DR PROSITE; PS51078; ICLR_ED; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-binding; Glyoxylate bypass; Reference proteome;
KW Repressor; Transcription; Transcription regulation.
FT CHAIN 1..274
FT /note="Transcriptional repressor IclR"
FT /id="PRO_0000201758"
FT DOMAIN 24..86
FT /note="HTH iclR-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00393"
FT DOMAIN 101..272
FT /note="IclR-ED"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00394"
FT DNA_BIND 46..65
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00393"
FT BINDING 160..161
FT /ligand="glyoxylate"
FT /ligand_id="ChEBI:CHEBI:36655"
FT BINDING 212
FT /ligand="glyoxylate"
FT /ligand_id="ChEBI:CHEBI:36655"
FT BINDING 222
FT /ligand="glyoxylate"
FT /ligand_id="ChEBI:CHEBI:36655"
FT BINDING 239..241
FT /ligand="glyoxylate"
FT /ligand_id="ChEBI:CHEBI:36655"
FT MUTAGEN 143
FT /note="L->D: Strongly reduced promoter binding and
FT tetramerization."
FT /evidence="ECO:0000269|PubMed:17426033"
FT MUTAGEN 146
FT /note="M->D: Strongly reduced promoter binding and
FT tetramerization."
FT /evidence="ECO:0000269|PubMed:17426033"
FT MUTAGEN 154
FT /note="L->D: Strongly reduced promoter binding and
FT tetramerization."
FT /evidence="ECO:0000269|PubMed:17426033"
FT MUTAGEN 220
FT /note="L->D: Loss of promoter binding and tetramerization."
FT /evidence="ECO:0000269|PubMed:17426033"
FT HELIX 99..116
FT /evidence="ECO:0007829|PDB:2O99"
FT STRAND 118..126
FT /evidence="ECO:0007829|PDB:2O99"
FT TURN 127..130
FT /evidence="ECO:0007829|PDB:2O99"
FT STRAND 131..138
FT /evidence="ECO:0007829|PDB:2O99"
FT STRAND 143..146
FT /evidence="ECO:0007829|PDB:2O99"
FT STRAND 156..159
FT /evidence="ECO:0007829|PDB:2O99"
FT HELIX 160..166
FT /evidence="ECO:0007829|PDB:2O99"
FT HELIX 171..175
FT /evidence="ECO:0007829|PDB:2O99"
FT HELIX 177..180
FT /evidence="ECO:0007829|PDB:2O99"
FT HELIX 194..207
FT /evidence="ECO:0007829|PDB:2O99"
FT STRAND 209..217
FT /evidence="ECO:0007829|PDB:2O99"
FT STRAND 220..228
FT /evidence="ECO:0007829|PDB:2O99"
FT STRAND 230..232
FT /evidence="ECO:0007829|PDB:1TD5"
FT STRAND 234..243
FT /evidence="ECO:0007829|PDB:2O99"
FT TURN 244..246
FT /evidence="ECO:0007829|PDB:2O99"
FT HELIX 249..251
FT /evidence="ECO:0007829|PDB:2O99"
FT HELIX 252..273
FT /evidence="ECO:0007829|PDB:2O99"
SQ SEQUENCE 274 AA; 29739 MW; 7C8A7E9FD2841D0C CRC64;
MVAPIPAKRG RKPAVATAPA TGQVQSLTRG LKLLEWIAES NGSVALTELA QQAGLPNSTT
HRLLTTMQQQ GFVRQVGELG HWAIGAHAFM VGSSFLQSRN LLAIVHPILR NLMEESGETV
NMAVLDQSDH EAIIIDQVQC THLMRMSAPI GGKLPMHASG AGKAFLAQLS EEQVTKLLHR
KGLHAYTHAT LVSPVHLKED LAQTRKRGYS FDDEEHALGL RCLAACIFDE HREPFAAISI
SGPISRITDD RVTEFGAMVI KAAKEVTLAY GGMR
