Escherichia coli K-12 substr. MG1655 Polypeptide: predicted DNA topoisomerase

Gene: yrdD Accession Numbers: G7699 (EcoCyc), b3283, ECK3270

Regulation Summary Diagram: ?

Regulation summary diagram for yrdD

YrdD has sequence similarity to the C-terminal zinc-binding region of DNA topoisomerase I. Purified YrdD contains both zinc and iron ions, but only the zinc-bound form is able to bind ssDNA [Cheng14].

An insertion mutant of yrdD was isolated as a suppressor of the rdgB recA(Ts) near-lethal phenotype. As with endonuclease V (Nfi), it is thought that the suppressor effect is due to decreased excision of base analogues (which would normally be removed by RdgB) from DNA and thus a decreased numbers of double-strand breaks (with would normally be repaired by RecA) [Budke10].

Gene Citations: [Kaczanowska04, Kaczanowska05]

Locations: cytosol

Map Position: [3,429,442 <- 3,429,984] (73.92 centisomes, 266°)
Length: 543 bp / 180 aa

Molecular Weight of Polypeptide: 19.871 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010768 , DIP:DIP-12917N , EchoBASE:EB2690 , EcoGene:EG12841 , EcoliWiki:b3283 , Mint:MINT-1244363 , OU-Microarray:b3283 , PortEco:yrdD , Pride:P45771 , Protein Model Portal:P45771 , RefSeq:YP_026210 , RegulonDB:G7699 , String:511145.b3283 , UniProt:P45771

Relationship Links: InterPro:IN-FAMILY:IPR000380 , InterPro:IN-FAMILY:IPR013498 , Panther:IN-FAMILY:PTHR11390 , Pfam:IN-FAMILY:PF01396

GO Terms:

Biological Process: GO:0006265 - DNA topological change Inferred by computational analysis [GOA01]
Molecular Function: GO:0003697 - single-stranded DNA binding Inferred from experiment [Cheng14]
GO:0005506 - iron ion binding Inferred from experiment [Cheng14]
GO:0008270 - zinc ion binding Inferred from experiment [Cheng14]
GO:0003677 - DNA binding Inferred by computational analysis [GOA01]
GO:0003916 - DNA topoisomerase activity Inferred by computational analysis [GOA01]
GO:0003917 - DNA topoisomerase type I activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005694 - chromosome Inferred by computational analysis [GOA01]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

Gene Class: ORFs Conserved-ORFs

Essentiality data for yrdD 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]

Curated 05-Jan-2006 by Shearer A , SRI International
Last-Curated ? 04-Feb-2014 by Keseler I , SRI International

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Suzanne Paley on Thu Oct 21, 2004:
Position updated based on U00096.2 release of genome
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

Budke10: Budke B, Kuzminov A (2010). "Production of clastogenic DNA precursors by the nucleotide metabolism in Escherichia coli." Mol Microbiol 75(1);230-45. PMID: 19943897

Cheng14: Cheng Z, Tan G, Wang W, Su X, Landry AP, Lu J, Ding H (2014). "Iron and zinc binding activity of Escherichia coli topoisomerase I homolog YrdD." Biometals. PMID: 24469504

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

GOA01: 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

Kaczanowska04: Kaczanowska M, Ryden-Aulin M (2004). "Temperature sensitivity caused by mutant release factor 1 is suppressed by mutations that affect 16S rRNA maturation." J Bacteriol 186(10);3046-55. PMID: 15126466

Kaczanowska05: Kaczanowska M, Ryden-Aulin M (2005). "The YrdC protein--a putative ribosome maturation factor." Biochim Biophys Acta 1727(2);87-96. PMID: 15716138

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 Fri Oct 9, 2015, biocyc13.