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Escherichia coli K-12 substr. MG1655 Protein: DsdC DNA-binding transcriptional dual regulator



Gene: dsdC Accession Numbers: EG13161 (EcoCyc), b2364, ECK2360

Regulation Summary Diagram: ?

Component of: DsdC-D-serine DNA binding transcriptional dual regulator (summary available)

Subunit composition of DsdC DNA-binding transcriptional dual regulator = [DsdC]2
         DsdC DNA-binding transcriptional dual regulator = DsdC

Citations: [McFall83, NorregaardMadse95]

Gene Citations: [Carothers80, BornsteinForst87, NorregaardMadse95]

Locations: cytosol

Map Position: [2,474,716 <- 2,475,651] (53.34 centisomes)
Length: 936 bp / 311 aa

Molecular Weight of Polypeptide: 35.332 kD (from nucleotide sequence)

pI: 6.88

Unification Links: ASAP:ABE-0007797 , DIP:DIP-9480N , EchoBASE:EB2953 , EcoGene:EG13161 , EcoliWiki:b2364 , ModBase:P46068 , OU-Microarray:b2364 , PortEco:dsdC , PR:PRO_000022486 , Protein Model Portal:P46068 , RefSeq:NP_416865 , RegulonDB:EG13161 , SMR:P46068 , String:511145.b2364 , UniProt:P46068

Relationship Links: EcoO157Cyc:Homolog:Z0885 , EcoO157Cyc:Homolog:Z0885-MONOMER , InterPro:IN-FAMILY:IPR000847 , InterPro:IN-FAMILY:IPR005119 , InterPro:IN-FAMILY:IPR011781 , InterPro:IN-FAMILY:IPR011991 , Pfam:IN-FAMILY:PF00126 , Pfam:IN-FAMILY:PF03466 , Prints:IN-FAMILY:PR00039 , Prosite:IN-FAMILY:PS50931

In Paralogous Gene Group: 6 (42 members)

In Reactions of unknown directionality:

Not in pathways:
DsdC + D-serine = DsdC DNA-binding transcriptional dual regulator

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005737 - cytoplasm
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
metabolism carbon utilization amino acids
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor

Symmetry: Inverted Repeat

Essentiality data for dsdC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Created 27-Jun-2008 by Gama-Castro S , UNAM


Subunit of: DsdC-D-serine DNA binding transcriptional dual regulator

Subunit composition of DsdC-D-serine DNA binding transcriptional dual regulator = [(DsdC)2][D-serine]
         DsdC DNA-binding transcriptional dual regulator = (DsdC)2
                 DsdC DNA-binding transcriptional dual regulator = DsdC

Summary:
In the presence of d-serine, the "D-serine deaminase" protein, DsdC, activates the transcription of genes involved in d-serine detoxification, and in the absence of the metabolite it is autorepressed [McFall83].

DsbC belongs to the LysR family of bacterial transcriptional regulators and contains a possible helix-turn-helix motif for DNA binding in the C-terminal domain. This protein shows 50% similarity to the GcvA protein [NorregaardMadse95, Palchaudhuri88].

The dsbC gene is located next to an operon ( dsdXA ) regulated by DsbC, but facing in the opposite direction. The activation effect of DsdC on this operon is enhanced by CRP, but CRP cannot act alone on the operon [NorregaardMadse95].

A DNA-binding site recognized by the dimer of DsbC has not been identified.

Sequence Length: 311 AAs

In Reactions of unknown directionality:

Not in pathways:
DsdC + D-serine = DsdC DNA-binding transcriptional dual regulator

GO Terms:

Biological Process: GO:0045893 - positive regulation of transcription, DNA-templated Inferred from experiment [Heincz78]
Molecular Function: GO:0070905 - serine binding Inferred from experiment [Heincz78]

MultiFun Terms: information transfer RNA related Transcription related
metabolism carbon utilization amino acids
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor

Credits:
Last-Curated ? 15-Aug-2008 by Gama-Castro S , UNAM

Symmetry: Inverted Repeat

Regulated Transcription Units (3 total): ?

Notes:


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 15 -> 72
[UniProt09]
UniProt: HTH lysR-type;
DNA-Binding-Region 32 -> 51
[UniProt10a]
UniProt: H-T-H motif; Non-Experimental Qualifier: potential;
Sequence-Conflict 159
[NorregaardMadse95, UniProt10]
Alternate sequence: A → R; UniProt: (in Ref. 1; CAA62931);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
1/26/1998 (pkarp) Merged genes G7987/dsdC and EG13161/dsdC


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

BornsteinForst87: Bornstein-Forst SM, McFall E, Palchaudhuri S (1987). "In vivo D-serine deaminase transcription start sites in wild-type Escherichia coli and in dsdA promoter mutants." J Bacteriol 1987;169(3);1056-60. PMID: 3029015

Carothers80: Carothers AM, McFall E, Palchaudhuri S (1980). "Physical mapping of the Escherichia coli D-serine deaminase region: contiguity of the dsd structural and regulatory genes." J Bacteriol 1980;142(1);174-84. PMID: 6246062

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

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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

Heincz78: Heincz MC, McFall E (1978). "Role of the dsdC activator in regulation of D-serine deaminase synthesis." J Bacteriol 136(1);96-103. PMID: 213419

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

McFall83: McFall E, Heincz MC (1983). "Identification and control of synthesis of the dsdC activator protein." J Bacteriol 1983;153(2);872-7. PMID: 6296057

NorregaardMadse95: Norregaard-Madsen M, McFall E, Valentin-Hansen P (1995). "Organization and transcriptional regulation of the Escherichia coli K-12 D-serine tolerance locus." J Bacteriol 1995;177(22);6456-61. PMID: 7592420

Palchaudhuri88: Palchaudhuri S, Patel V, McFall E (1988). "DNA sequence of the D-serine deaminase activator gene dsdC." J Bacteriol 170(1);330-4. PMID: 3275618

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

Other References Related to Gene Regulation

Huerta03: Huerta AM, Collado-Vides J (2003). "Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals." J Mol Biol 333(2);261-78. PMID: 14529615

Partridge09: Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S (2009). "NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility." Mol Microbiol 73(4);680-94. PMID: 19656291


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 Nov 23, 2014, biocyc13.