P0ACN4 (ALLR_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
HTH-type transcriptional repressor AllR

Alternative name(s):
Negative regulator of allantoin and glyoxylate utilization operons

Gene names

Name:	allR
Synonyms:	glxA3, ybbU
Ordered Locus Names:	b0506, JW0494

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	271 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Negative regulator of allantoin and glyoxylate utilization operons. Binds to the gcl promoter and to the allS-allA intergenic region. Binding to DNA is abolished by glyoxylate. Ref.1 Ref.5 Ref.6
Subunit structure	Homotetramer and homodimer. Homotetramer in its active, DNA-bound form. Homodimer in its inactive form. Ref.6
Sequence similarities	Contains 1 HTH iclR-type DNA-binding domain. Contains 1 iclR-ED (iclR effector binding) domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Ligand	DNA-binding
Molecular function	Repressor
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	negative regulation of transcription, DNA-dependent Inferred from direct assay Ref.1Ref.6. Source: EcoCyc response to DNA damage stimulus Inferred from expression pattern PubMed 11967071. Source: EcoliWiki transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW sequence-specific DNA binding transcription factor activity Inferred from direct assay Ref.1Ref.6. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 271

271

HTH-type transcriptional repressor AllR

PRO_0000201753

Regions

Domain

21 – 83

63

HTH iclR-type

Domain

98 – 267

170

IclR-ED

DNA binding

43 – 62

20

H-T-H motif Potential

Region

154 – 156

3

Glyoxylate binding

Region

234 – 236

3

Glyoxylate binding

Sites

Binding site

207

1

Glyoxylate

Binding site

217

1

Glyoxylate

Experimental info

Mutagenesis

135 – 142

8

CKSMVRMC → APA: Loss of repressor activity. Loss of DNA binding. Reduces assembly into functionally active tetramers. Ref.6

Mutagenesis

141

1

M → A: No effect on repressor activity. Loss of glyoxylate-triggered dissociation from DNA. Ref.6

Mutagenesis

142

1

C → W: Strongly reduced repressor activity. Reduces DNA binding. Prevents assembly into functionally active tetramers. Ref.6

Mutagenesis

215

1

L → A: Reduced repressor activity. Loss of glyoxylate-triggered dissociation from DNA. Ref.6

Mutagenesis

217

1

C → A or S: Slightly reduced repressor activity. Loss of glyoxylate-triggered dissociation from DNA. Ref.6

Mutagenesis

234

1

S → A or N: Reduced repressor activity. Loss of glyoxylate-triggered dissociation from DNA. Ref.6

Mutagenesis

236

1

S → A or M: Slightly reduced repressor activity. Loss of glyoxylate-triggered dissociation from DNA. Ref.6

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

271

Helix Strand Turn

Details...

Helix

97 – 113

17

Beta strand

115 – 123

9

Beta strand

126 – 133

8

Beta strand

138 – 141

4

Beta strand

148 – 150

3

Turn

151 – 153

3

Helix

155 – 161

7

Helix

166 – 176

11

Helix

189 – 202

14

Beta strand

205 – 212

8

Beta strand

215 – 223

9

Beta strand

229 – 238

10

Turn

239 – 241

3

Helix

244 – 246

3

Helix

247 – 265

19

Sequences

	Sequence		Length	Mass (Da)
	P0ACN4 [UniParc]. Last modified November 22, 2005. Version 1. Checksum: 476F59EEC0F8308B	FASTA	271	29,270
	10 20 30 40 50 60 MTEVRRRGRP GQAEPVAQKG AQALERGIAI LQYLEKSGGS SSVSDISLNL DLPLSTTFRL 70 80 90 100 110 120 LKVLQAADFV YQDSQLGWWH IGLGVFNVGA AYIHNRDVLS VAGPFMRRLM LLSGETVNVA 130 140 150 160 170 180 IRNGNEAVLI GQLECKSMVR MCAPLGSRLP LHASGAGKAL LYPLAEEELM SIILQTGLQQ 190 200 210 220 230 240 FTPTTLVDMP TLLKDLEQAR ELGYTVDKEE HVVGLNCIAS AIYDDVGSVV AAISISGPSS 250 260 270 RLTEDRFVSQ GELVRDTARD ISTALGLKAH P

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Genetic analysis of a chromosomal region containing genes required for assimilation of allantoin nitrogen and linked glyoxylate metabolism in Escherichia coli." Cusa E., Obradors N., Baldoma L., Badia J., Aguilar J. J. Bacteriol. 181:7479-7484(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION. Strain: K12 / ECL1.
[2]	"Sequence of minutes 4-25 of Escherichia coli." Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W. Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Regulation of the Escherichia coli allantoin regulon: coordinated function of the repressor AllR and the activator AllS." Rintoul M.R., Cusa E., Baldoma L., Badia J., Reitzer L., Aguilar J. J. Mol. Biol. 324:599-610(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, DNA-BINDING. Strain: K12.
[6]	"Structural and biochemical study of effector molecule recognition by the E.coli glyoxylate and allantoin utilization regulatory protein AllR." Walker J.R., Altamentova S., Ezersky A., Lorca G., Skarina T., Kudritska M., Ball L.J., Bochkarev A., Savchenko A. J. Mol. Biol. 358:810-828(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 97-271 IN COMPLEX WITH GLYOXALATE, FUNCTION, SUBUNIT, MUTAGENESIS OF 135-CYS--CYS-142; MET-141; CYS-142; LEU-215; CYS-217; SER-234 AND SER-236. Strain: K12 / BW25113.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U89024 Genomic DNA. Translation: AAB93847.1.
U82664 Genomic DNA. Translation: AAB40259.1.
U00096 Genomic DNA. Translation: AAC73608.1.
AP009048 Genomic DNA. Translation: BAE76284.1.

PIR

A64782.

RefSeq

NP_415039.1. NC_000913.2.
YP_488796.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1TF1	X-ray	1.80	A/B/C/D	97-271	[»]

ProteinModelPortal

P0ACN4.

SMR

P0ACN4. Positions 23-269.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-47907N.

IntAct

P0ACN4. 20 interactions.

STRING

511145.b0506.

Proteomic databases

PaxDb

P0ACN4.

PRIDE

P0ACN4.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73608; AAC73608; b0506.
BAE76284; BAE76284; BAE76284.

GeneID

12930877.
945333.

KEGG

ecj:Y75_p0492.
eco:b0506.

PATRIC

32116171. VBIEscCol129921_0527.

Organism-specific databases

EchoBASE

EB3382.

EcoGene

EG13616. allR.

Phylogenomic databases

eggNOG

COG1414.

HOGENOM

HOG000107041.

KO

K10973.

OMA

YLHICAS.

ProtClustDB

PRK10163.

Enzyme and pathway databases

BioCyc

EcoCyc:G6276-MONOMER.
ECOL316407:JW0494-MONOMER.

Gene expression databases

Genevestigator

P0ACN4.

Family and domain databases

Gene3D

1.10.10.10. 1 hit.

InterPro

IPR014757. Tscrpt_reg_IclR_C.
IPR005471. Tscrpt_reg_IclR_N.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]

Pfam

PF09339. HTH_IclR. 1 hit.
PF01614. IclR. 1 hit.
[Graphical view]

SMART

SM00346. HTH_ICLR. 1 hit.
[Graphical view]

PROSITE

PS51077. HTH_ICLR. 1 hit.
PS51078. ICLR_ED. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0ACN4.

Entry information

Entry name

ALLR_ECOLI

Accession

Primary (citable) accession number: P0ACN4
Secondary accession number(s): P77734, Q2MBS2

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 22, 2005
Last sequence update:	November 22, 2005
Last modified:	May 1, 2013
This is version 74 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program