Escherichia coli K-12 substr. MG1655 Enzyme: XTPase / ITPase

Gene: yjjX Accession Numbers: EG12600 (EcoCyc), b4394, ECK4386

Regulation Summary Diagram: ?

Regulation summary diagram for yjjX

Subunit composition of XTPase / ITPase = [YjjX]2
         ITPase/XTPase = YjjX

YjjX is a phosphatase that preferentially hydrolyzes inosine triphosphate (ITP) and xanthosine triphosphate (XTP). Both ITP and XTP can be formed by oxidative deamination damage, converting an amino group of adenine or guanine to a keto group. By hydrolyzing these damaged nucleotides, YjjX may thus prevent their incorporation into RNA [Zheng05].

A crystal structure of YjjX has been solved at 2.3 Å resolution; the protein forms a dimer in the crystal structure as well as in solution [Zheng05].

Overexpression of YjjX from a multicopy plasmid leads to resistance to the HMP (4-amino-2-methyl-5-hydroxymethylpyrimidine) analog CF3-HMP (4-amino-2-trifluoromethyl-5-hydroxymethylpyrimidine). The resistance mechanism is undetermined, but does not involve biosynthesis of HMP [Lawhorn04]. Overexpression of yjjX also suppresses the rdgB recA(Ts) near-lethal phenotype, presumably by substituting for RdgB activity [Budke10].

Review: [Rao05]

Locations: cytosol

Map Position: [4,631,256 <- 4,631,768] (99.82 centisomes, 359°)
Length: 513 bp / 170 aa

Molecular Weight of Polypeptide: 18.213 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0014411 , DIP:DIP-12663N , EchoBASE:EB2485 , EcoGene:EG12600 , EcoliWiki:b4394 , OU-Microarray:b4394 , PortEco:yjjX , Pride:P39411 , Protein Model Portal:P39411 , RefSeq:NP_418811 , RegulonDB:EG12600 , SMR:P39411 , String:511145.b4394 , UniProt:P39411

Relationship Links: InterPro:IN-FAMILY:IPR002786 , InterPro:IN-FAMILY:IPR026533 , InterPro:IN-FAMILY:IPR029001 , PDB:Structure:1U5W , Pfam:IN-FAMILY:PF01931

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006772 - thiamine metabolic process Inferred from experiment [Lawhorn04]
GO:0009117 - nucleotide metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0046677 - response to antibiotic Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0017111 - nucleoside-triphosphatase activity Inferred from experiment Inferred by computational analysis [GOA06, Zheng05]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes protection detoxification

Essentiality data for yjjX 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]
Yes [Feist07, Comment 4]

Created 07-Mar-2006 by Keseler I , SRI International
Last-Curated ? 11-Dec-2009 by Keseler I , SRI International

Enzymatic reaction of: XTPase

EC Number: 3.6.1.-

XTP + H2O <=> XDP + 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.

Cofactors or Prosthetic Groups: Mg2+

Kinetic Parameters:

Km (μM)

pH(opt): 6.75 [Zheng05]

Enzymatic reaction of: ITPase

EC Number: 3.6.1.-

ITP + H2O <=> IDP + 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 ITP: dITP [Zheng05 ]

dITP is also a substrate, but with a 10-fold higher Km of 4.51 mM [Zheng05].

Cofactors or Prosthetic Groups: Mg2+

Inhibitors (Competitive): ATP [Zheng05] , GTP [Zheng05] , thiamin diphosphate [Zheng05]

Kinetic Parameters:

Km (μM)

pH(opt): 6.75 [Zheng05]

Sequence Features

Protein sequence of ITPase/XTPase with features indicated

Feature Class Location Citations Comment
Protein-Segment 8 -> 13
[UniProt, 2012]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Metal-Binding-Site 38
[UniProt, 2012]
UniProt: Manganese or magnesium; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 68
[UniProt, 2012]
UniProt: Manganese or magnesium; Non-Experimental Qualifier: by similarity.
Protein-Segment 68 -> 69
[UniProt, 2012]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Sequence-Conflict 146 -> 152
[Skrypka94, UniProt10a]
UniProt: (in Ref. 5; AAA72135);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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 ].
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 ].
10/20/97 Gene b4394 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12600; confirmed by SwissProt match.


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

Budke10: Budke B, Kuzminov A (2010). "Production of clastogenic DNA precursors by the nucleotide metabolism in Escherichia coli." Mol Microbiol 75(1);230-45. PMID: 19943897

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

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

Lawhorn04: Lawhorn BG, Gerdes SY, Begley TP (2004). "A genetic screen for the identification of thiamin metabolic genes." J Biol Chem 279(42);43555-9. PMID: 15292217

Rao05: Rao Z (2005). "YjjX: from structure "Tu" function." Structure 13(10);1401-2. PMID: 16216571

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

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

Skrypka94: Skrypka I, Somerville RL (1994). "Nucleotide sequence of the Salmonella typhimurium trpR gene." DNA Seq 4(6);355-60. PMID: 7841459

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

Zheng05: Zheng J, Singh VK, Jia Z (2005). "Identification of an ITPase/XTPase in Escherichia coli by structural and biochemical analysis." Structure 13(10);1511-20. PMID: 16216582

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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 Fri Mar 27, 2015, biocyc14.