Escherichia coli K-12 substr. MG1655 Polypeptide: ribosome-binding ATPase, inhibitor of catalase activity

Gene: ychF Accession Numbers: EG11404 (EcoCyc), b1203, ECK1191

Synonyms: gtp1

Regulation Summary Diagram: ?

Regulation summary diagram for ychF

The highly conserved YchF protein has K+-activated ATPase activity and binds to both the 70S ribosome and the 50S ribosomal subunit in a nucleotide-independent manner [Tomar11]. Nucleotide binding to YchF induces different conformational states. The KD of the YchF·ADPNP complex for 70S ribosomes is 3 µM, and the 70S ribosome stimulates the ATPase activity fo YchF [Becker12].

In the presence of hydrogen peroxide (H2O2), overexpressed YchF was found to interact directly with the major catalase KatG and to inhibit its activity. Treatment of cells with H2O2 increases the ATPase activity of YchF; the function of YchF may be controlled by phosphorylation and perhaps additional modifications [Wenk12].

YchF is a monomer in solution [Tomar11].

YchF is the founding member of a family of GTP-binding proteins [Mittenhuber01] with ATPase activity [KollerEichhorn07]. The bacterial GTPase superfamily is associated with RNA- and translation-related roles in the cell [Caldon01].

A ychF null mutant strain has a slow growth phenotype [Arigoni98] and is more sensitive to kasugamycin than wild type [Skunca13]. Overexpression of ychF results in hypersensitivity to hydrogen peroxide, and transcription of ychF is down-regulated by OxyR in response to oxidative stress [Wenk12].

Reviews: [Mittenhuber01, Caldon01, Brown05a, Verstraeten11]

Citations: [Wang12g]

Gene Citations: [CruzVera02]

Map Position: [1,255,944 <- 1,257,035] (27.07 centisomes, 97°)
Length: 1092 bp / 363 aa

Molecular Weight of Polypeptide: 39.667 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004038 , EchoBASE:EB1376 , EcoGene:EG11404 , EcoliWiki:b1203 , ModBase:P0ABU2 , OU-Microarray:b1203 , PortEco:ychF , PR:PRO_000022517 , Pride:P0ABU2 , Protein Model Portal:P0ABU2 , RefSeq:NP_415721 , RegulonDB:EG11404 , SMR:P0ABU2 , String:511145.b1203 , Swiss-Model:P0ABU2 , UniProt:P0ABU2

Relationship Links: InterPro:IN-FAMILY:IPR004396 , InterPro:IN-FAMILY:IPR006073 , InterPro:IN-FAMILY:IPR012675 , InterPro:IN-FAMILY:IPR012676 , InterPro:IN-FAMILY:IPR013029 , InterPro:IN-FAMILY:IPR023192 , InterPro:IN-FAMILY:IPR027417 , Panther:IN-FAMILY:PTHR23305:SF4 , Pfam:IN-FAMILY:PF01926 , Pfam:IN-FAMILY:PF06071 , Prints:IN-FAMILY:PR00326 , Prosite:IN-FAMILY:PS51710

Genetic Regulation Schematic: ?

Genetic regulation schematic for ychF

GO Terms:

Biological Process: GO:0006979 - response to oxidative stress Inferred from experiment [Wenk12]
GO:0008152 - metabolic process Inferred from experiment Inferred by computational analysis [GOA06, Tomar11]
GO:0043086 - negative regulation of catalytic activity Inferred from experiment [Wenk12]
Molecular Function: GO:0004857 - enzyme inhibitor activity Inferred from experiment [Wenk12]
GO:0005515 - protein binding Inferred from experiment [Wenk12]
GO:0016887 - ATPase activity Inferred from experiment Inferred by computational analysis [GOA06, Tomar11]
GO:0043022 - ribosome binding Inferred from experiment Inferred by computational analysis [GOA06, Tomar11]
GO:0043023 - ribosomal large subunit binding Inferred from experiment Inferred by computational analysis [GOA06, Tomar11]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0005525 - GTP binding Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: information transfer protein related translation

Essentiality data for ychF 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]

Last-Curated ? 12-Nov-2012 by Keseler I , SRI International

Sequence Features

Protein sequence of ribosome-binding ATPase, inhibitor of catalase activity with features indicated

Feature Class Location Attached Group Citations Comment
Cleavage-of-Initial-Methionine 1  
[Link97, UniProt11]
UniProt: Removed.
Chain 2 -> 363  
UniProt: GTP-dependent nucleic acid-binding protein engD;
Conserved-Region 3 -> 256  
UniProt: OBG-type G.
Nucleotide-Phosphate-Binding-Region 12 -> 17 ATP
UniProt: ATP; Non-Experimental Qualifier: by similarity.
Mutagenesis-Variant 12  
[Tomar11, UniProt13]
UniProt: Shows similar hydrolysis activities in the presence of K(+) or Na(+).
Metal-Binding-Site 16  
UniProt: Magnesium.
Metal-Binding-Site 36  
UniProt: Magnesium.
Mutagenesis-Variant 78  
[Tomar11, UniProt13]
[Tomar11, UniProt13]
K → R: Retains K(+)-dependent stimulation of ATPase activity and differentiates between K(+) and Na(+).
K → A: Shows similar hydrolysis activities in the presence of K(+) or Na(+).

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b1203 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11404; confirmed by SwissProt match.


Arigoni98: Arigoni F, Talabot F, Peitsch M, Edgerton MD, Meldrum E, Allet E, Fish R, Jamotte T, Curchod ML, Loferer H (1998). "A genome-based approach for the identification of essential bacterial genes." Nat Biotechnol 16(9);851-6. PMID: 9743119

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

Becker12: Becker M, Gzyl KE, Altamirano AM, Vuong A, Urban K, Wieden HJ (2012). "The 70S ribosome modulates the ATPase activity of Escherichia coli YchF." RNA Biol 9(10). PMID: 22995830

Brown05a: Brown ED (2005). "Conserved P-loop GTPases of unknown function in bacteria: an emerging and vital ensemble in bacterial physiology." Biochem Cell Biol 83(6);738-46. PMID: 16333325

Caldon01: Caldon CE, Yoong P, March PE (2001). "Evolution of a molecular switch: universal bacterial GTPases regulate ribosome function." Mol Microbiol 41(2);289-97. PMID: 11489118

CruzVera02: Cruz-Vera LR, Galindo JM, Guarneros G (2002). "Transcriptional analysis of the gene encoding peptidyl-tRNA hydrolase in Escherichia coli." Microbiology 148(Pt 11);3457-66. PMID: 12427937

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

KollerEichhorn07: Koller-Eichhorn R, Marquardt T, Gail R, Wittinghofer A, Kostrewa D, Kutay U, Kambach C (2007). "Human OLA1 defines an ATPase subfamily in the Obg family of GTP-binding proteins." J Biol Chem 282(27);19928-37. PMID: 17430889

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

Mittenhuber01: Mittenhuber G (2001). "Comparative genomics of prokaryotic GTP-binding proteins (the Era, Obg, EngA, ThdF (TrmE), YchF and YihA families) and their relationship to eukaryotic GTP-binding proteins (the DRG, ARF, RAB, RAN, RAS and RHO families)." J Mol Microbiol Biotechnol 2001;3(1);21-35. PMID: 11200227

Skunca13: Skunca N, Bošnjak M, Kriško A, Panov P, Džeroski S, Smuc T, Supek F (2013). "Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships." PLoS Comput Biol 9(1);e1002852. PMID: 23308060

Tomar11: Tomar SK, Kumar P, Prakash B (2011). "Deciphering the catalytic machinery in a universally conserved ribosome binding ATPase YchF." Biochem Biophys Res Commun 408(3);459-64. PMID: 21527254

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

UniProt14: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-01 00:00:00." Database.

UniProt14a: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

Verstraeten11: Verstraeten N, Fauvart M, Versees W, Michiels J (2011). "The universally conserved prokaryotic GTPases." Microbiol Mol Biol Rev 75(3);507-42, second and third pages of table of contents. PMID: 21885683

Wang12g: Wang X, Xue J, Sun Z, Qin Y, Gong W (2012). "Study on the chaperone properties of conserved GTPases." Protein Cell 3(1);44-50. PMID: 22246579

Wenk12: Wenk M, Ba Q, Erichsen V, Macinnes K, Wiese H, Warscheid B, Koch HG (2012). "A Universally Conserved ATPase Regulates the Oxidative Stress Response in Escherichia coli." J Biol Chem 287(52);43585-98. PMID: 23139412

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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.