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



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

Synonyms: yffD

Regulation Summary Diagram: ?

Component of: GcvR-gly (summary available)

Gene Citations: [Ghrist98]

Locations: cytosol

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

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

Unification Links: ASAP:ABE-0008168 , 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: ?

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

Summary:
"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 [Ghrist95a, 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 [Ghrist95a]
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

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Ghrist98, UniProt11]
UniProt: Removed.
Chain 2 -> 190
[UniProt09]
UniProt: Glycine cleavage system transcriptional repressor;
Conserved-Region 10 -> 91
[UniProt13]
UniProt: ACT 1.
Conserved-Region 97 -> 176
[UniProt13]
UniProt: ACT 2.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
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.


References

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

Ghrist95a: 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 18.5 on Sun Dec 21, 2014, biocyc14.