Escherichia coli K-12 substr. MG1655 Polypeptide: GcvR predicted transcriptional regulator

Gene: gcvR Accession Numbers: EG11149 (EcoCyc), b2479, ECK2475

Synonyms: yffD

Regulation Summary Diagram: ?

Regulation summary diagram for gcvR

Component of: GcvR-gly (summary available)

Gene Citations: [Ghrist98]

Locations: cytosol

Map Position: [2,597,928 -> 2,598,500] (55.99 centisomes, 202°)
Length: 573 bp / 190 aa

Molecular Weight of Polypeptide: 20.769 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008168 , DIP:DIP-9754N , EchoBASE:EB1138 , EcoGene:EG11149 , EcoliWiki:b2479 , ModBase:P0A9I3 , OU-Microarray:b2479 , PortEco:gcvR , PR:PRO_000022765 , Pride:P0A9I3 , Protein Model Portal:P0A9I3 , RefSeq:NP_416974 , RegulonDB:EG11149 , SMR:P0A9I3 , String:511145.b2479 , Swiss-Model:P0A9I3 , UniProt:P0A9I3

Relationship Links: InterPro:IN-FAMILY:IPR002912 , InterPro:IN-FAMILY:IPR016867 , Pfam:IN-FAMILY:PF01842 , Prosite:IN-FAMILY:PS51671

In Reactions of unknown directionality:

Not in pathways:
GcvR + glycine = GcvR-gly

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11, Heil02]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0016597 - amino acid binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

MultiFun Terms: information transfer RNA related Transcription related
metabolism carbon utilization amino acids
metabolism central intermediary metabolism formyl-THF biosynthesis
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor

Symmetry: Inverted Repeat

Essentiality data for gcvR knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Subunit of: GcvR-gly

Synonyms: YffD, B2479, GcvR

Subunit composition of GcvR-gly = [GcvR][glycine]
         GcvR predicted transcriptional regulator = GcvR

"Glycine cleavage repressor," GcvR, is an accessory protein that binds directly to GcvA, bending DNA to form a repression complex (GcvA/GcvR) in the regulatory region of the gcvT operon [Ghrist95, Ghrist01].

Glycine binds directly to GcvR to disrupt or block the association of the GcvA/GcvR complex, whereas purines appear to promote the formation of the repression complex through an unknown mechanism [Heil02, Ghrist01]. In the absence of glycine and the presence of GcvR, the GcvA/GcvR complex represses the operon involved in the glycine cleavage enzyme system [Ghrist01].

Sequence Length: 190 AAs

Molecular Weight: 20.769 kD (from nucleotide sequence)

Relationship Links: Pfam:IN-FAMILY:PF01842

In Reactions of unknown directionality:

Not in pathways:
GcvR + glycine = GcvR-gly

GO Terms:

Biological Process: GO:0010629 - negative regulation of gene expression Inferred from experiment [Ghrist95]
Molecular Function: GO:0008134 - transcription factor binding Inferred from experiment [Ghrist01]
GO:0016594 - glycine binding Inferred from experiment [Heil02]

MultiFun Terms: information transfer RNA related Transcription related
metabolism carbon utilization amino acids
metabolism central intermediary metabolism formyl-THF biosynthesis
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor

Sequence Features

Protein sequence of GcvR predicted transcriptional regulator with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Ghrist98, UniProt11]
UniProt: Removed.
Chain 2 -> 190
UniProt: Glycine cleavage system transcriptional repressor;
Conserved-Region 10 -> 91
UniProt: ACT 1.
Conserved-Region 97 -> 176
UniProt: ACT 2.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


Socorro Gama-Castro on Fri Apr 29, 2005:
The start site of this gene was originally assigned solely on the basis of sequence considerations [Blattner97 ] . However, it was changed because Ghrist and Stauffer [3 ] attested that the real start site is actually located 66 bp downstream. The demonstration is based on the sequence of the first 14 amino acids and the identification of both a plausible ribosome binding site and a promoter at an appropriate distance from the new start site. The transcription start site was identified using primer extension analysis.
Suzanne Paley on Thu Oct 21, 2004:
Position updated based on U00096.2 release of genome
10/20/97 Gene b2479 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11149; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Blattner97: Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997). "The complete genome sequence of Escherichia coli K-12." Science 277(5331);1453-74. PMID: 9278503

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Ghrist01: Ghrist AC, Heil G, Stauffer GV (2001). "GcvR interacts with GcvA to inhibit activation of the Escherichia coli glycine cleavage operon." Microbiology 147(Pt 8);2215-21. PMID: 11495998

Ghrist95: Ghrist AC, Stauffer GV (1995). "Characterization of the Escherichia coli gcvR gene encoding a negative regulator of gcv expression." J Bacteriol 177(17);4980-4. PMID: 7665475

Ghrist98: Ghrist AC, Stauffer GV (1998). "Promoter characterization and constitutive expression of the Escherichia coli gcvR gene." J Bacteriol 1998;180(7);1803-7. PMID: 9537378

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Heil02: Heil G, Stauffer LT, Stauffer GV (2002). "Glycine binds the transcriptional accessory protein GcvR to disrupt a GcvA/GcvR interaction and allow GcvA-mediated activation of the Escherichia coli gcvTHP operon." Microbiology 148(Pt 7);2203-14. PMID: 12101307

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Mon Oct 5, 2015, biocyc12.