Escherichia coli K-12 substr. MG1655 Enzyme: O-acetyl-ADP-ribose deacetylase, regulator of RNase III activity

Gene: ymdB Accession Numbers: G6550 (EcoCyc), b1045, ECK1031

Regulation Summary Diagram: ?

Regulation summary diagram for ymdB

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].

Locations: cytosol

Map Position: [1,105,043 -> 1,105,576] (23.82 centisomes, 86°)
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

Relationship Links: InterPro:IN-FAMILY:IPR002589 , InterPro:IN-FAMILY:IPR024900 , PDB:Structure:1SPV , Pfam:IN-FAMILY:PF01661 , Prosite:IN-FAMILY:PS51154 , Smart:IN-FAMILY:SM00506

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0032074 - negative regulation of nuclease activity Inferred from experiment [Kim08]
GO:1900231 - regulation of single-species biofilm formation on inanimate substrate Inferred from experiment [Kim13b]
GO:0042278 - purine nucleoside metabolic process Inferred by computational analysis [GOA06]
GO:0060701 - negative regulation of ribonuclease activity Inferred by computational analysis [GOA06]
Molecular Function: GO:0008428 - ribonuclease inhibitor activity Inferred from experiment Inferred by computational analysis [GOA06, Kim08]
GO:0019899 - enzyme binding Inferred from experiment [Kim08]
GO:0061463 - O-acetyl-ADP-ribose deacetylase activity Inferred from experiment [Chen11]
GO:0001883 - purine nucleoside binding Inferred by computational analysis [GOA06]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0019213 - deacetylase activity Inferred by computational analysis [GOA06]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: regulation type of regulation posttranscriptional inhibition / activation of enzymes

Essentiality data for ymdB 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]

Created 11-Feb-2009 by Keseler I , SRI International
Last-Curated ? 04-Dec-2013 by Keseler I , SRI International

Enzymatic reaction of: O-acetyl-ADP-ribose deacetylase

an O-acetyl-ADP-ribose + H2O <=> ADP-D-ribose + acetate

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.

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
an O-acetyl-ADP-ribose

Sequence Features

Protein sequence of O-acetyl-ADP-ribose deacetylase, regulator of RNase III activity with features indicated

Feature Class Location Citations Comment
Conserved-Region 1 -> 175
UniProt: Macro;
Active-Site 35
UniProt: Proton acceptor; Non-Experimental Qualifier: potential.
Protein-Segment 121 -> 127
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: probable.
Mutagenesis-Variant 124
[Chen11, UniProt12b]
UniProt: Abolishes enzyme activity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


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

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

Kim08: Kim KS, Manasherob R, Cohen SN (2008). "YmdB: a stress-responsive ribonuclease-binding regulator of E. coli RNase III activity." Genes Dev 22(24);3497-508. PMID: 19141481

Kim13b: Kim T, Lee J, Kim KS (2013). "Escherichia coli YmdB regulates biofilm formation independently of its role as an RNase III modulator." BMC Microbiol 13;266. PMID: 24267348

Makarov92: Makarov EM, Apirion D (1992). "10Sa RNA: processing by and inhibition of RNase III." Biochem Int 26(6);1115-24. PMID: 1378735

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

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

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

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProt12b: UniProt Consortium (2012). "UniProt version 2012-02 released on 2012-02-29 00:00:00." Database.

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

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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 Thu Oct 8, 2015, biocyc13.