Acetate operon repressor - Escherichia coli (strain K12)

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P16528 (ICLR_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 118. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Acetate operon repressor

Gene names

Name:	iclR
Ordered Locus Names:	b4018, JW3978

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	274 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Regulation of the glyoxylate bypass operon (aceBAK), which encodes isocitrate lyase, malate synthase as well as isocitrate dehydrogenase kinase/phosphorylase. Glyoxylate disrupts the interaction with the promoter by favoring the inactive dimeric form. Pyruvate enhances promoter binding by stabilizing the tetrameric form.
Subunit structure	Homotetramer and homodimer. Homotetramer in its active, DNA-bound form. Homodimer in its inactive form. Ref.7
Miscellaneous	Glyoxylate and pyruvate occupy the same site.
Sequence similarities	Contains 1 HTH iclR-type DNA-binding domain. Contains 1 iclR-ED (iclR effector binding) domain.
Sequence caution	The sequence AAA50561.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened. The sequence AAC43112.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Biological process	Glyoxylate bypass Transcription Transcription regulation
Ligand	DNA-binding
Molecular function	Repressor
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	glyoxylate cycle Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from mutant phenotype PubMed 7033207. Source: EcoCyc transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
hldD	P67910	1	EBI-552904,EBI-543760
rpsC	P0A7V3	1	EBI-552904,EBI-544851

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 274

274

Acetate operon repressor

PRO_0000201758

Regions

Domain

24 – 86

HTH iclR-type

Domain

101 – 272

172

IclR-ED

DNA binding

46 – 65

H-T-H motif Potential

Region

160 – 161

Glyoxylate binding

Region

239 – 241

Glyoxylate binding

Sites

Binding site

212

Glyoxylate

Binding site

222

Glyoxylate

Experimental info

Mutagenesis

143

L → D: Strongly reduced promoter binding and tetramerization. Ref.7

Mutagenesis

146

M → D: Strongly reduced promoter binding and tetramerization. Ref.7

Mutagenesis

154

L → D: Strongly reduced promoter binding and tetramerization. Ref.7

Mutagenesis

220

L → D: Loss of promoter binding and tetramerization. Ref.7

Secondary structure

274

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P16528 [UniParc].

Last modified August 1, 1990. Version 1.
Checksum: 7C8A7E9FD2841D0C
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FASTA

274

29,739

        10         20         30         40         50         60 
MVAPIPAKRG RKPAVATAPA TGQVQSLTRG LKLLEWIAES NGSVALTELA QQAGLPNSTT 

        70         80         90        100        110        120 
HRLLTTMQQQ GFVRQVGELG HWAIGAHAFM VGSSFLQSRN LLAIVHPILR NLMEESGETV 

       130        140        150        160        170        180 
NMAVLDQSDH EAIIIDQVQC THLMRMSAPI GGKLPMHASG AGKAFLAQLS EEQVTKLLHR 

       190        200        210        220        230        240 
KGLHAYTHAT LVSPVHLKED LAQTRKRGYS FDDEEHALGL RCLAACIFDE HREPFAAISI 

       250        260        270 
SGPISRITDD RVTEFGAMVI KAAKEVTLAY GGMR

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Regulation of the glyoxylate bypass operon: cloning and characterization of iclR." Sunnarborg A., Klumpp D.J., Chung T., Laporte D.C. J. Bacteriol. 172:2642-2649(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Overproduction and characterization of the iclR gene product of Escherichia coli K-12 and comparison with that of Salmonella typhimurium LT2." Negre D., Cortay J.-C., Old I.G., Galinier A., Richaud C., Saint-Girons I., Cozzone A.J. Gene 97:29-37(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[3]	"Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes." Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L. Nucleic Acids Res. 21:5408-5417(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"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.
[5]	"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.
[6]	"Primary structure of the intergenic region between aceK and iclR in the Escherichia coli chromosome." Galinier A., Bleicher F., Negre D., Perriere G., Duclos B., Cozzone A.J., Cortay J.-C. Gene 97:149-150(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 262-274.
[7]	"Glyoxylate and pyruvate are antagonistic effectors of the Escherichia coli IclR transcriptional regulator." Lorca G.L., Ezersky A., Lunin V.V., Walker J.R., Altamentova S., Evdokimova E., Vedadi M., Bochkarev A., Savchenko A. J. Biol. Chem. 282:16476-16491(2007) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 98-274 IN COMPLEXES WITH PYRUVATE AND GLYOXYLATE, SUBUNIT, MUTAGENESIS OF LEU-143; MET-146; LEU-154 AND LEU-220.
[8]	"Crystal structure analysis of the E. coli glyoxylate regulatory protein ligand binding domain." Walker J.R., Skarina T., Kudrytska M., Arrowsmith C., Edwards A., Savchenko A. Submitted (JAN-2005) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 98-274.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M31761 Genomic DNA. Translation: AAA24008.1.
M63914 Genomic DNA. Translation: AAA50561.1. Different initiation.
U00006 Genomic DNA. Translation: AAC43112.1. Different initiation.
U00096 Genomic DNA. Translation: AAC76988.2.
AP009048 Genomic DNA. Translation: BAE78020.1.
M63497 Genomic DNA. Translation: AAA73003.1.

RefSeq

NP_418442.2. NC_000913.2.
YP_492161.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1TD5	X-ray	2.30	A/B/C/D	98-274	[»]
2O99	X-ray	1.70	A/B/C/D	98-274	[»]
2O9A	X-ray	1.80	A/B/C/D	98-274	[»]

ProteinModelPortal

P16528.

SMR

P16528. Positions 24-274.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10008N.

IntAct

P16528. 17 interactions.

MINT

MINT-1226737.

STRING

511145.b4018.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76988; AAC76988; b4018.
BAE78020; BAE78020; BAE78020.

GeneID

12934466.
948524.

KEGG

ecj:Y75_p3905.
eco:b4018.

PATRIC

32123565. VBIEscCol129921_4131.

Organism-specific databases

EchoBASE

EB0486.

EcoGene

EG10491. iclR.

Phylogenomic databases

eggNOG

COG1414.

HOGENOM

HOG000107041.

K13641.

OMA

KMISTIQ.

ProtClustDB

PRK11569.

Enzyme and pathway databases

BioCyc

EcoCyc:PD04099.
ECOL316407:JW3978-MONOMER.

Gene expression databases

Genevestigator

P16528.

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

P16528.

Entry information

Entry name

ICLR_ECOLI

Accession

Primary (citable) accession number: P16528
Secondary accession number(s): P76782, Q2M6T6

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1990
Last sequence update:	August 1, 1990
Last modified:	May 1, 2013
This is version 118 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents