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Escherichia coli K-12 substr. MG1655 Enzyme: ribonucleoside hydrolase 3



Gene: rihC Accession Numbers: EG11082 (EcoCyc), b0030, ECK0031

Synonyms: yaaF

Regulation Summary Diagram: ?

Summary:
rihC encodes a ribonucleoside hydrolase with a broad substrate specificity. It has decreasing activity on substrates in the order uridine > xanthosine > inosine > adenosine > cytidine [Petersen01]. The enzyme has no activity with deoxyribonucleosides [Petersen01]. E. coli contains two other nucleoside hydrolases with differing specificities, encoded by rihA and rihB [Petersen01].

The transition state of the enzyme has been modeled based on kinetic isotope effects [Hunt05]. Potential active and catalytic sites and the catalytic mechanism of RihC have been computationally predicted [Farone10].

An rihA rihB rihC triple mutant does not exhibit an obvious growth defect [Petersen01].

The rihA and rihC genes are subject to catabolite repression [Petersen01]. Transcription is induced by nalidixic acid, but not by mitomycin C, and induction does not require LexA [Van01].

Locations: cytosol

Map Position: [27,293 -> 28,207] (0.59 centisomes)
Length: 915 bp / 304 aa

Molecular Weight of Polypeptide: 32.561 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0000109 , DIP:DIP-11157N , EchoBASE:EB1074 , EcoGene:EG11082 , EcoliWiki:b0030 , Mint:MINT-1268238 , ModBase:P22564 , OU-Microarray:b0030 , PortEco:rihC , PR:PRO_000023758 , Protein Model Portal:P22564 , RefSeq:NP_414571 , RegulonDB:EG11082 , SMR:P22564 , String:511145.b0030 , Swiss-Model:P22564 , UniProt:P22564

Relationship Links: InterPro:IN-FAMILY:IPR001910 , InterPro:IN-FAMILY:IPR015910 , InterPro:IN-FAMILY:IPR022976 , InterPro:IN-FAMILY:IPR023186 , Panther:IN-FAMILY:PTHR12304 , Pfam:IN-FAMILY:PF01156 , Prosite:IN-FAMILY:PS01247

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0042454 - ribonucleoside catabolic process Inferred from experiment [Petersen01]
GO:0006144 - purine nucleobase metabolic process Inferred by computational analysis [GOA06]
GO:0006206 - pyrimidine nucleobase metabolic process Inferred by computational analysis [GOA06]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0045437 - uridine nucleosidase activity Inferred from experiment [Hunt05]
GO:0047622 - adenosine nucleosidase activity Inferred from experiment [Petersen01]
GO:0047724 - inosine nucleosidase activity Inferred from experiment [Petersen01]
GO:0050263 - ribosylpyrimidine nucleosidase activity Inferred from experiment [Petersen01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016798 - hydrolase activity, acting on glycosyl bonds Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0016799 - hydrolase activity, hydrolyzing N-glycosyl compounds Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism central intermediary metabolism nucleotide and nucleoside conversions

Essentiality data for rihC 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]

Credits:
Curated 28-Sep-2010 by Keseler I , SRI International
Last-Curated ? 01-Dec-2011 by Fulcher C , SRI International


Enzymatic reaction of: uridine nucleosidase (ribonucleoside hydrolase 3)

EC Number: 3.2.2.3

uridine + H2O <=> D-ribofuranose + uracil

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 irreversible in the direction shown.

In Pathways: superpathway of pyrimidine ribonucleosides salvage , pyrimidine ribonucleosides salvage II


Enzymatic reaction of: xanthosine nucleosidase (ribonucleoside hydrolase 3)

EC Number: 3.2.2.1

xanthosine + H2O <=> D-ribofuranose + xanthine

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.


Enzymatic reaction of: inosine nucleosidase (ribonucleoside hydrolase 3)

EC Number: 3.2.2.2

inosine + H2O <=> D-ribofuranose + hypoxanthine

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.


Enzymatic reaction of: adenosine nucleosidase (ribonucleoside hydrolase 3)

EC Number: 3.2.2.7

adenosine + H2O <=> D-ribofuranose + adenine

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.

In Pathways: adenine and adenosine salvage II


Enzymatic reaction of: cytidine nucleosidase (ribonucleoside hydrolase 3)

EC Number: 3.2.2.3

cytidine + H2O <=> D-ribofuranose + cytosine

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

In Pathways: pyrimidine ribonucleosides salvage III


Sequence Features

Feature Class Location Citations Comment
Active-Site 233
[UniProt10a]
UniProt: Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b0030 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11082; confirmed by SwissProt match.


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

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

Farone10: Farone A, Farone M, Kline P, Quinn T, Sinkala Z (2010). "A Practical Approach for Computing the Active Site of the Ribonucleoside Hydrolase of E. coli Encoded by rihC." Adv Exp Med Biol 680;437-43. PMID: 20865528

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

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."

Hunt05: Hunt C, Gillani N, Farone A, Rezaei M, Kline PC (2005). "Kinetic isotope effects of nucleoside hydrolase from Escherichia coli." Biochim Biophys Acta 1751(2);140-9. PMID: 16027052

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

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Petersen01: Petersen C, Moller LB (2001). "The RihA, RihB, and RihC ribonucleoside hydrolases of Escherichia coli. Substrate specificity, gene expression, and regulation." J Biol Chem 2001;276(2);884-94. PMID: 11027694

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

Van01: Van Dyk TK, DeRose EJ, Gonye GE (2001). "LuxArray, a high-density, genomewide transcription analysis of Escherichia coli using bioluminescent reporter strains." J Bacteriol 183(19);5496-505. PMID: 11544210


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 Sun Nov 23, 2014, BIOCYC14B.