ALLR_ECOLI
ID ALLR_ECOLI Reviewed; 271 AA.
AC P0ACN4; P77734; Q2MBS2;
DT 22-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT 22-NOV-2005, sequence version 1.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=HTH-type transcriptional repressor AllR;
DE AltName: Full=Negative regulator of allantoin and glyoxylate utilization operons;
GN Name=allR; Synonyms=glxA3, ybbU; OrderedLocusNames=b0506, JW0494;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RC STRAIN=K12 / ECL1;
RX PubMed=10601204; DOI=10.1128/jb.181.24.7479-7484.1999;
RA Cusa E., Obradors N., Baldoma L., Badia J., Aguilar J.;
RT "Genetic analysis of a chromosomal region containing genes required for
RT assimilation of allantoin nitrogen and linked glyoxylate metabolism in
RT Escherichia coli.";
RL J. Bacteriol. 181:7479-7484(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [3]
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 [4]
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 [5]
RP FUNCTION, AND DNA-BINDING.
RC STRAIN=K12;
RX PubMed=12460564; DOI=10.1016/s0022-2836(02)01134-8;
RA Rintoul M.R., Cusa E., Baldoma L., Badia J., Reitzer L., Aguilar J.;
RT "Regulation of the Escherichia coli allantoin regulon: coordinated function
RT of the repressor AllR and the activator AllS.";
RL J. Mol. Biol. 324:599-610(2002).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 97-271 IN COMPLEX WITH GLYOXALATE,
RP FUNCTION, SUBUNIT, AND MUTAGENESIS OF 135-CYS--CYS-142; MET-141; CYS-142;
RP LEU-215; CYS-217; SER-234 AND SER-236.
RC STRAIN=K12 / BW25113;
RX PubMed=16546208; DOI=10.1016/j.jmb.2006.02.034;
RA Walker J.R., Altamentova S., Ezersky A., Lorca G., Skarina T.,
RA Kudritska M., Ball L.J., Bochkarev A., Savchenko A.;
RT "Structural and biochemical study of effector molecule recognition by the
RT E.coli glyoxylate and allantoin utilization regulatory protein AllR.";
RL J. Mol. Biol. 358:810-828(2006).
CC -!- FUNCTION: Negative regulator of allantoin and glyoxylate utilization
CC operons. Binds to the gcl promoter and to the allS-allA intergenic
CC region. Binding to DNA is abolished by glyoxylate.
CC {ECO:0000269|PubMed:10601204, ECO:0000269|PubMed:12460564,
CC ECO:0000269|PubMed:16546208}.
CC -!- SUBUNIT: Homotetramer and homodimer. Homotetramer in its active, DNA-
CC bound form. Homodimer in its inactive form.
CC {ECO:0000269|PubMed:16546208}.
CC -!- INTERACTION:
CC P0ACN4; P0ACN4: allR; NbExp=4; IntAct=EBI-561736, EBI-561736;
CC P0ACN4; P31552: caiC; NbExp=3; IntAct=EBI-561736, EBI-1112975;
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DR EMBL; U89024; AAB93847.1; -; Genomic_DNA.
DR EMBL; U82664; AAB40259.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73608.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76284.1; -; Genomic_DNA.
DR PIR; A64782; A64782.
DR RefSeq; NP_415039.1; NC_000913.3.
DR RefSeq; WP_000141275.1; NZ_STEB01000007.1.
DR PDB; 1TF1; X-ray; 1.80 A; A/B/C/D=97-271.
DR PDBsum; 1TF1; -.
DR AlphaFoldDB; P0ACN4; -.
DR SMR; P0ACN4; -.
DR BioGRID; 4259871; 7.
DR BioGRID; 849709; 2.
DR DIP; DIP-47907N; -.
DR IntAct; P0ACN4; 21.
DR STRING; 511145.b0506; -.
DR jPOST; P0ACN4; -.
DR PaxDb; P0ACN4; -.
DR PRIDE; P0ACN4; -.
DR EnsemblBacteria; AAC73608; AAC73608; b0506.
DR EnsemblBacteria; BAE76284; BAE76284; BAE76284.
DR GeneID; 67416416; -.
DR GeneID; 945333; -.
DR KEGG; ecj:JW0494; -.
DR KEGG; eco:b0506; -.
DR PATRIC; fig|1411691.4.peg.1771; -.
DR EchoBASE; EB3382; -.
DR eggNOG; COG1414; Bacteria.
DR HOGENOM; CLU_062618_7_1_6; -.
DR InParanoid; P0ACN4; -.
DR OMA; DTTETIH; -.
DR PhylomeDB; P0ACN4; -.
DR BioCyc; EcoCyc:G6276-MON; -.
DR EvolutionaryTrace; P0ACN4; -.
DR PRO; PR:P0ACN4; -.
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; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IEP:EcoliWiki.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IDA: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; Reference proteome; Repressor; Transcription;
KW Transcription regulation.
FT CHAIN 1..271
FT /note="HTH-type transcriptional repressor AllR"
FT /id="PRO_0000201753"
FT DOMAIN 21..83
FT /note="HTH iclR-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00393"
FT DOMAIN 98..267
FT /note="IclR-ED"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00394"
FT DNA_BIND 43..62
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00393"
FT BINDING 154..156
FT /ligand="glyoxylate"
FT /ligand_id="ChEBI:CHEBI:36655"
FT BINDING 207
FT /ligand="glyoxylate"
FT /ligand_id="ChEBI:CHEBI:36655"
FT BINDING 217
FT /ligand="glyoxylate"
FT /ligand_id="ChEBI:CHEBI:36655"
FT BINDING 234..236
FT /ligand="glyoxylate"
FT /ligand_id="ChEBI:CHEBI:36655"
FT MUTAGEN 135..142
FT /note="CKSMVRMC->APA: Loss of repressor activity. Loss of
FT DNA binding. Reduces assembly into functionally active
FT tetramers."
FT /evidence="ECO:0000269|PubMed:16546208"
FT MUTAGEN 141
FT /note="M->A: No effect on repressor activity. Loss of
FT glyoxylate-triggered dissociation from DNA."
FT /evidence="ECO:0000269|PubMed:16546208"
FT MUTAGEN 142
FT /note="C->W: Strongly reduced repressor activity. Reduces
FT DNA binding. Prevents assembly into functionally active
FT tetramers."
FT /evidence="ECO:0000269|PubMed:16546208"
FT MUTAGEN 215
FT /note="L->A: Reduced repressor activity. Loss of
FT glyoxylate-triggered dissociation from DNA."
FT /evidence="ECO:0000269|PubMed:16546208"
FT MUTAGEN 217
FT /note="C->A,S: Slightly reduced repressor activity. Loss of
FT glyoxylate-triggered dissociation from DNA."
FT /evidence="ECO:0000269|PubMed:16546208"
FT MUTAGEN 234
FT /note="S->A,N: Reduced repressor activity. Loss of
FT glyoxylate-triggered dissociation from DNA."
FT /evidence="ECO:0000269|PubMed:16546208"
FT MUTAGEN 236
FT /note="S->A,M: Slightly reduced repressor activity. Loss of
FT glyoxylate-triggered dissociation from DNA."
FT /evidence="ECO:0000269|PubMed:16546208"
FT HELIX 97..113
FT /evidence="ECO:0007829|PDB:1TF1"
FT STRAND 115..123
FT /evidence="ECO:0007829|PDB:1TF1"
FT STRAND 126..133
FT /evidence="ECO:0007829|PDB:1TF1"
FT STRAND 138..141
FT /evidence="ECO:0007829|PDB:1TF1"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:1TF1"
FT TURN 151..153
FT /evidence="ECO:0007829|PDB:1TF1"
FT HELIX 155..161
FT /evidence="ECO:0007829|PDB:1TF1"
FT HELIX 166..176
FT /evidence="ECO:0007829|PDB:1TF1"
FT HELIX 189..202
FT /evidence="ECO:0007829|PDB:1TF1"
FT STRAND 205..212
FT /evidence="ECO:0007829|PDB:1TF1"
FT STRAND 215..223
FT /evidence="ECO:0007829|PDB:1TF1"
FT STRAND 229..238
FT /evidence="ECO:0007829|PDB:1TF1"
FT TURN 239..241
FT /evidence="ECO:0007829|PDB:1TF1"
FT HELIX 244..246
FT /evidence="ECO:0007829|PDB:1TF1"
FT HELIX 247..265
FT /evidence="ECO:0007829|PDB:1TF1"
SQ SEQUENCE 271 AA; 29270 MW; 476F59EEC0F8308B CRC64;
MTEVRRRGRP GQAEPVAQKG AQALERGIAI LQYLEKSGGS SSVSDISLNL DLPLSTTFRL
LKVLQAADFV YQDSQLGWWH IGLGVFNVGA AYIHNRDVLS VAGPFMRRLM LLSGETVNVA
IRNGNEAVLI GQLECKSMVR MCAPLGSRLP LHASGAGKAL LYPLAEEELM SIILQTGLQQ
FTPTTLVDMP TLLKDLEQAR ELGYTVDKEE HVVGLNCIAS AIYDDVGSVV AAISISGPSS
RLTEDRFVSQ GELVRDTARD ISTALGLKAH P
