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discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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Escherichia coli K-12 substr. MG1655 Polypeptide: ATP-dependent dsDNA exonuclease



Gene: sbcD Accession Numbers: EG11094 (EcoCyc), b0398, ECK0392

Synonyms: yajA

Regulation Summary Diagram: ?

Component of: SbcCD ATP-dependent dsDNA exonuclease (summary available)

Summary:
The sbcC and sbcD genes mediate palindrome inviability in E. coli. sbcD encodes a component of the SbcCD exonuclease [Connelly96].

Gene Citations: [Darmon07]

Locations: cytosol

Map Position: [414,974 <- 416,176] (8.94 centisomes)
Length: 1203 bp / 400 aa

Molecular Weight of Polypeptide: 44.714 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0001383 , CGSC:30972 , EchoBASE:EB1086 , EcoGene:EG11094 , EcoliWiki:b0398 , ModBase:P0AG76 , OU-Microarray:b0398 , PortEco:sbcD , PR:PRO_000023911 , Protein Model Portal:P0AG76 , RefSeq:NP_414932 , RegulonDB:EG11094 , SMR:P0AG76 , String:511145.b0398 , UniProt:P0AG76

Relationship Links: InterPro:IN-FAMILY:IPR004593 , InterPro:IN-FAMILY:IPR004843 , InterPro:IN-FAMILY:IPR026843 , Pfam:IN-FAMILY:PF00149 , Pfam:IN-FAMILY:PF12320

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006259 - DNA metabolic process Inferred from experiment Inferred by computational analysis [GOA01a, Connelly97]
GO:0006260 - DNA replication Inferred by computational analysis [UniProtGOA11a]
GO:0006310 - DNA recombination Inferred by computational analysis [UniProtGOA11a]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0004519 - endonuclease activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0004527 - exonuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0008408 - 3'-5' exonuclease activity Inferred by computational analysis [GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer DNA related DNA degradation
metabolism degradation of macromolecules DNA

Essentiality data for sbcD 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:
Revised 25-May-2011 by Brito D


Subunit of: SbcCD ATP-dependent dsDNA exonuclease

Subunit composition of SbcCD ATP-dependent dsDNA exonuclease = [SbcC][SbcD]
         ATP-dependent dsDNA exonuclease = SbcC (extended summary available)
         ATP-dependent dsDNA exonuclease = SbcD (summary available)

Summary:

Credits:
Created 05-Apr-2006 by Johnson A , TIGR


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0398 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11094; 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

Connelly96: Connelly JC, Leach DR (1996). "The sbcC and sbcD genes of Escherichia coli encode a nuclease involved in palindrome inviability and genetic recombination." Genes Cells 1(3);285-91. PMID: 9133662

Connelly97: Connelly JC, de Leau ES, Okely EA, Leach DR (1997). "Overexpression, purification, and characterization of the SbcCD protein from Escherichia coli." J Biol Chem 272(32);19819-26. PMID: 9242643

Connelly98: Connelly JC, Kirkham LA, Leach DR (1998). "The SbcCD nuclease of Escherichia coli is a structural maintenance of chromosomes (SMC) family protein that cleaves hairpin DNA." Proc Natl Acad Sci U S A 95(14);7969-74. PMID: 9653124

Connelly99: Connelly JC, de Leau ES, Leach DR (1999). "DNA cleavage and degradation by the SbcCD protein complex from Escherichia coli." Nucleic Acids Res 27(4);1039-46. PMID: 9927737

Darmon07: Darmon E, Lopez-Vernaza MA, Helness AC, Borking A, Wilson E, Thacker Z, Wardrope L, Leach DR (2007). "SbcCD regulation and localization in Escherichia coli." J Bacteriol 189(18);6686-94. PMID: 17644583

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

Gibson92: Gibson FP, Leach DR, Lloyd RG (1992). "Identification of sbcD mutations as cosuppressors of recBC that allow propagation of DNA palindromes in Escherichia coli K-12." J Bacteriol 174(4);1222-8. PMID: 1531222

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

Lloyd85: Lloyd RG, Buckman C (1985). "Identification and genetic analysis of sbcC mutations in commonly used recBC sbcB strains of Escherichia coli K-12." J Bacteriol 164(2);836-44. PMID: 3932331

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

Other References Related to Gene Regulation

Harley87: Harley CB, Reynolds RP (1987). "Analysis of E. coli promoter sequences." Nucleic Acids Res 15(5);2343-61. PMID: 3550697

Makino86: Makino K, Shinagawa H, Amemura M, Nakata A (1986). "Nucleotide sequence of the phoB gene, the positive regulatory gene for the phosphate regulon of Escherichia coli K-12." J Mol Biol 1986;190(1);37-44. PMID: 3537313

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360

Naom89: Naom IS, Morton SJ, Leach DR, Lloyd RG (1989). "Molecular organization of sbcC, a gene that affects genetic recombination and the viability of DNA palindromes in Escherichia coli K-12." Nucleic Acids Res 17(20);8033-45. PMID: 2530497

Yang12: Yang C, Huang TW, Wen SY, Chang CY, Tsai SF, Wu WF, Chang CH (2012). "Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli." PLoS One 7(10);e47314. PMID: 23071782


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 Mon Dec 22, 2014, biocyc11.