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Escherichia coli K-12 substr. MG1655 Enzyme: regulatory ATPase



Gene: ravA Accession Numbers: EG11731 (EcoCyc), b3746, ECK3740

Synonyms: yieN

Regulation Summary Diagram: ?

Subunit composition of regulatory ATPase = [RavA]6
         regulatory ATPase = RavA

Summary:
RavA belongs to the MoxR family of AAA+ ATPases. In the presence of ATP, RavA forms a hexamer [Snider06].

RavA interacts with the inducible lysine decarboxylase (CadA), but not LdcC; interaction with CadA stimulates the ATPase activity of RavA [Snider06]. Interaction with RavA reduces the inhibitory effect of the alarmone ppGpp on CadA activity [El10].

A crystal structure of RavA with ADP bound has been solved at 2.9 Å resolution [El10]. RavA consists of a conserved N-terminal AAA+ domain and a poorly conserved C-terminal domain [Snider06] which is formed by a discontinuous triple-helical domain and the LARA domain, which mediates the interaction with CadA [El10].

Analysis of microarray and synthetic genetic array data suggests a functional link between RavA and Fe-S cluster protein homeostasis as well as bacterial respiration [Wong14].

Expression of RavA is under control of the alternative sigma factor σS; RavA levels increase in late log/early stationary phase [Snider06]. A ravA mutant reaches a higher cell density in stationary phase than wild type in the presence of sublethal levels of the aminoglycosides kanamycin or streptomycin; conversely, overexpression of RavA sensitizes cells to kanamycin. Deletion of certain subunits of NADH:ubiquinone oxidoreductase I, SDH and cytochrome bo suppress this effect [Wong14].

RavA: "regulatory ATPase variant A" [Snider06]

Review: [Wong12]

Locations: cytosol

Map Position: [3,927,620 <- 3,929,116] (84.65 centisomes)
Length: 1497 bp / 498 aa

Molecular Weight of Polypeptide: 56.389 kD (from nucleotide sequence)

Molecular Weight of Multimer: 310 kD (experimental) [Snider06]

Unification Links: ASAP:ABE-0012247 , DIP:DIP-12469N , EchoBASE:EB1682 , EcoGene:EG11731 , EcoliWiki:b3746 , Mint:MINT-1242859 , ModBase:P31473 , OU-Microarray:b3746 , PortEco:ravA , PR:PRO_000023680 , Pride:P31473 , Protein Model Portal:P31473 , RefSeq:NP_418202 , RegulonDB:EG11731 , SMR:P31473 , String:511145.b3746 , UniProt:P31473

Relationship Links: InterPro:IN-FAMILY:IPR003593 , InterPro:IN-FAMILY:IPR011704 , InterPro:IN-FAMILY:IPR022547 , InterPro:IN-FAMILY:IPR023671 , InterPro:IN-FAMILY:IPR027417 , PDB:Structure:3NBX , Pfam:IN-FAMILY:PF07728 , Pfam:IN-FAMILY:PF12592 , Smart:IN-FAMILY:SM00382

In Paralogous Gene Group: 105 (10 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006200 - ATP catabolic process Inferred by computational analysis Inferred from experiment [Snider06, GOA01a]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0055085 - transmembrane transport Inferred by computational analysis [GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Snider06, Butland05]
GO:0016887 - ATPase activity Inferred from experiment Inferred by computational analysis [GOA01a, Snider06]
GO:0042802 - identical protein binding Inferred from experiment [Snider06]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016820 - hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA01a, Snider06]
GO:0005829 - cytosol Inferred from experiment [Wong14]

MultiFun Terms: regulation type of regulation unknown

Essentiality data for ravA 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:
Created 05-Dec-2005 by Keseler I , SRI International
Last-Curated ? 28-Jan-2014 by Keseler I , SRI International


Enzymatic reaction of: ATPase

EC Number: 3.6.1.15

ATP + H2O <=> ADP + phosphate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for ATP: GTP [Snider06 ]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
ATP
790.0
1.4
[Snider06]

pH(opt): 7.5 [Snider06]


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b3746 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11731.


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

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

El10: El Bakkouri M, Gutsche I, Kanjee U, Zhao B, Yu M, Goret G, Schoehn G, Burmeister WP, Houry WA (2010). "Structure of RavA MoxR AAA+ protein reveals the design principles of a molecular cage modulating the inducible lysine decarboxylase activity." Proc Natl Acad Sci U S A 107(52);22499-504. PMID: 21148420

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

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

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Snider06: Snider J, Gutsche I, Lin M, Baby S, Cox B, Butland G, Greenblatt J, Emili A, Houry WA (2006). "Formation of a distinctive complex between the inducible bacterial lysine decarboxylase and a novel AAA+ ATPase." J Biol Chem 281;1532-1546. PMID: 16301313

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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

Wong12: Wong KS, Houry WA (2012). "Novel structural and functional insights into the MoxR family of AAA+ ATPases." J Struct Biol 179(2);211-21. PMID: 22491058

Wong14: Wong KS, Snider JD, Graham C, Greenblatt JF, Emili A, Babu M, Houry WA (2014). "The MoxR ATPase RavA and Its Cofactor ViaA Interact with the NADH:Ubiquinone Oxidoreductase I in Escherichia coli." PLoS One 9(1);e85529. PMID: 24454883

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305


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 Fri Dec 19, 2014, biocyc14.