Escherichia coli K-12 substr. MG1655 Enzyme: DLP12 prophage; lysozyme

Gene: rrrD Accession Numbers: G6310 (EcoCyc), b0555, ECK0546

Synonyms: lycV, ybcS

Regulation Summary Diagram: ?

Regulation summary diagram for rrrD

RrrD is an endolysin encoded by the cryptic lambdoid prophage DLP12 [Srividhya07].

Overexpression of RrrD leads to lysis of the cells [Srividhya07]. The effect of an rrrD deletion on biofilm formation is dependent on the strain background. An rrrD mutant is impaired in curli-based biofilm formation, which may be an indirect effect due to altered peptidoglycan metabolism [Toba11].

Map Position: [576,836 -> 577,333] (12.43 centisomes, 45°)
Length: 498 bp / 165 aa

Molecular Weight of Polypeptide: 17.972 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0001898 , EchoBASE:EB3399 , EcoGene:EG13635 , EcoliWiki:b0555 , ModBase:P78285 , OU-Microarray:b0555 , PortEco:ybcS , Pride:P78285 , Protein Model Portal:P78285 , RefSeq:NP_415087 , RegulonDB:G6310 , SMR:P78285 , String:511145.b0555 , UniProt:P78285

Relationship Links: CAZy:IN-FAMILY:GH24 , InterPro:IN-FAMILY:IPR002196 , InterPro:IN-FAMILY:IPR023346 , InterPro:IN-FAMILY:IPR023347 , Pfam:IN-FAMILY:PF00959

In Paralogous Gene Group: 314 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0044659 - cytolysis by virus of host cell Inferred from experiment [Srividhya07]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0009253 - peptidoglycan catabolic process Inferred by computational analysis [GOA01]
GO:0016998 - cell wall macromolecule catabolic process Inferred by computational analysis [GOA01]
GO:0019835 - cytolysis Inferred by computational analysis [UniProtGOA11]
GO:0042742 - defense response to bacterium Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0003796 - lysozyme activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Srividhya07]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0016798 - hydrolase activity, acting on glycosyl bonds Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: extrachromosomal prophage genes and phage related functions

Essentiality data for rrrD 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]

Curated 21-Feb-2006 by Shearer A , SRI International
Last-Curated ? 29-Sep-2011 by Keseler I , SRI International

Enzymatic reaction of: lysozyme

EC Number:

a peptidoglycan + H2O <=> a N-acetylmuramoyl-pentapeptide-diphosphoundecaprenol + N-acetyl-D-glucosamine

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Sequence Features

Protein sequence of DLP12 prophage; lysozyme with features indicated

Feature Class Location Common Name Citations Comment
Signal-Sequence 1 -> 21 predicted type I signal peptide
Active-Site 35  
UniProt: Proton donor; Non-Experimental Qualifier: by similarity;
Active-Site 44  
UniProt: Nucleophile; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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

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."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

Srividhya07: Srividhya KV, Krishnaswamy S (2007). "Sub classification and targeted characterization of prophage-encoded two-component cell lysis cassette." J Biosci 32(5);979-90. PMID: 17914239

Toba11: Toba FA, Thompson MG, Campbell BR, Junker LM, Rueggeberg KG, Hay AG (2011). "Role of DLP12 lysis genes in Escherichia coli biofilm formation." Microbiology 157(Pt 6);1640-50. PMID: 21415116

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

Rhodius05: Rhodius VA, Suh WC, Nonaka G, West J, Gross CA (2005). "Conserved and variable functions of the sigmaE stress response in related genomes." PLoS Biol 4(1);e2. PMID: 16336047

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 Wed Oct 7, 2015, biocyc14.