|Gene:||ymdB||Accession Numbers: G6550 (EcoCyc), b1045, ECK1031|
Subunit composition of
O-acetyl-ADP-ribose deacetylase, regulator of RNase III activity = [YmdB]2
O-acetyl-ADP-ribose deacetylase, regulator of RNase III activity = YmdB
YmdB is a macrodomain family protein with O-acetyl-ADP-ribose deacetylase activity [Chen11]. O-acetyl-ADP-ribose is produced by NAD+-dependent protein deacetylation.
The YmdB protein inhibits the acitivity of RNase III by interacting direcly with the enzyme. Amino acids 120-140 in the catalytic region of RNase III are necessary for YmdB binding [Kim08]. A protein inhibitor of RNase III was first identified by Makarov and Apirion [Makarov92].
Expression of ymdB increases in early stationary phase and during cold shock and is dependent on the alternative sigma factor RpoS (σS). Downregulation of RNase III activity during cold shock requires YmdB, while decreased RNase III activity during stationary phase does not appear to depend on YmdB [Kim08]. Genes whose expression is modulated by YmdB were identified by microarray analysis [Kim13b].
Overexpression of YmdB inhibits biofilm formation. This effect is independent of RNase III, and may be due to an interaction with RpoS [Kim13b].
Full complementation of a clsC mutant requires co-expression with ymdB [Tan12].
|Map Position: [1,105,043 -> 1,105,576] (23.82 centisomes)||Length: 534 bp / 177 aa|
Molecular Weight of Polypeptide: 18.88 kD (from nucleotide sequence)
Unification Links: ASAP:ABE-0003549 , DIP:DIP-48222N , EchoBASE:EB3633 , EcoGene:EG13874 , EcoliWiki:b1045 , ModBase:P0A8D6 , OU-Microarray:b1045 , PortEco:ymdB , Pride:P0A8D6 , Protein Model Portal:P0A8D6 , RefSeq:NP_415563 , RegulonDB:G6550 , SMR:P0A8D6 , String:511145.b1045 , UniProt:P0A8D6
|Biological Process:||GO:0032074 - negative regulation of nuclease activity
GO:1900231 - regulation of single-species biofilm formation on inanimate substrate [Kim13b]
GO:0006950 - response to stress [UniProtGOA11a]
GO:0042278 - purine nucleoside metabolic process [GOA06]
GO:0060701 - negative regulation of ribonuclease activity [GOA06]
|Molecular Function:||GO:0008428 - ribonuclease inhibitor activity
GO:0019899 - enzyme binding [Kim08]
GO:0061463 - O-acetyl-ADP-ribose deacetylase activity [Chen11]
GO:0001883 - purine nucleoside binding [GOA06]
GO:0016787 - hydrolase activity [UniProtGOA11a]
GO:0019213 - deacetylase activity [GOA06]
|Cellular Component:||GO:0005829 - cytosol [DiazMejia09]|
|MultiFun Terms:||regulation → type of regulation → posttranscriptional → inhibition / activation of enzymes|
|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]|
Enzymatic reaction of: O-acetyl-ADP-ribose deacetylase
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.
Reversibility of this reaction is unspecified.
|Conserved-Region||1 -> 175|
|Protein-Segment||121 -> 127|
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
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
Chen11: Chen D, Vollmar M, Rossi MN, Phillips C, Kraehenbuehl R, Slade D, Mehrotra PV, von Delft F, Crosthwaite SK, Gileadi O, Denu JM, Ahel I (2011). "Identification of macrodomain proteins as novel O-acetyl-ADP-ribose deacetylases." J Biol Chem 286(15);13261-71. PMID: 21257746
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
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
Tan12: Tan BK, Bogdanov M, Zhao J, Dowhan W, Raetz CR, Guan Z (2012). "Discovery of a cardiolipin synthase utilizing phosphatidylethanolamine and phosphatidylglycerol as substrates." Proc Natl Acad Sci U S A 109(41);16504-9. PMID: 22988102
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