Escherichia coli K-12 substr. MG1655 Enzyme: ribonucleoside hydrolase 1 (pyrimidine-specific)

Gene: rihA Accession Numbers: G6358 (EcoCyc), b0651, ECK0644

Synonyms: ybeK

Regulation Summary Diagram: ?

Regulation summary diagram for rihA

rihA encodes a ribonucleoside hydrolase that preferentially utilizes cytidine and uridine [Petersen01]. The kcat/KM for uridine is approximately 10 times higher than for cytidine, largely due to a lower KM value for uridine [Muzzolini06]. E. coli contains two other nucleoside hydrolases with differing specificities, encoded by rihB and rihC [Petersen01].

A crystal structure of RihA bound to the reaction product D-ribose has been solved at 1.8 Å resolution [Muzzolini06], and a structure of RihA bound to the competitive inhibitor 3,4-diaminophenyl-iminoribitol was solved at 2.1 Å resolution [Garau10].

A triple mutant lacking rihA, rihB and rihC grows normally. An rihA null mutant in a pyr cdd mutant background can not use cytidine as a source of pyrimidine. The rihA and rihC genes are subject to catabolite repression [Petersen01].

Locations: cytosol

Map Position: [682,700 <- 683,635] (14.71 centisomes, 53°)
Length: 936 bp / 311 aa

Molecular Weight of Polypeptide: 33.823 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0002227 , EchoBASE:EB2563 , EcoGene:EG12701 , EcoliWiki:b0651 , ModBase:P41409 , OU-Microarray:b0651 , PortEco:rihA , PR:PRO_000023756 , Pride:P41409 , Protein Model Portal:P41409 , RefSeq:NP_415184 , RegulonDB:G6358 , SMR:P41409 , String:511145.b0651 , Swiss-Model:P41409 , UniProt:P41409

Relationship Links: InterPro:IN-FAMILY:IPR001910 , InterPro:IN-FAMILY:IPR015910 , InterPro:IN-FAMILY:IPR022975 , InterPro:IN-FAMILY:IPR023186 , Panther:IN-FAMILY:PTHR12304 , PDB:Structure:1YOE , PDB:Structure:3G5I , Pfam:IN-FAMILY:PF01156 , Prosite:IN-FAMILY:PS01247

In Paralogous Gene Group: 30 (25 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0046133 - pyrimidine ribonucleoside catabolic process Inferred from experiment [Petersen01]
GO:0006152 - purine nucleoside catabolic process Inferred by computational analysis [Gaudet10]
GO:0006206 - pyrimidine nucleobase metabolic process Inferred by computational analysis [GOA06, GOA01a]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0015949 - nucleobase-containing small molecule interconversion Inferred by computational analysis [GOA01a]
Molecular Function: GO:0005509 - calcium ion binding Inferred from experiment [Muzzolini06, Garau10]
GO:0005515 - protein binding Inferred from experiment [Muzzolini06]
GO:0045437 - uridine nucleosidase activity Inferred from experiment Inferred by computational analysis [GOA01a, Muzzolini06]
GO:0047405 - pyrimidine-5'-nucleotide nucleosidase activity Inferred from experiment [Muzzolini06]
GO:0008477 - purine nucleosidase activity Inferred by computational analysis [Gaudet10]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016798 - hydrolase activity, acting on glycosyl bonds Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0016799 - hydrolase activity, hydrolyzing N-glycosyl compounds Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [GOA01a]
GO:0005829 - cytosol Inferred by computational analysis [Gaudet10, DiazMejia09]

MultiFun Terms: metabolism central intermediary metabolism nucleotide and nucleoside conversions

Essentiality data for rihA 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]

Last-Curated ? 28-Sep-2010 by Keseler I , SRI International

Enzymatic reaction of: uridine nucleosidase (ribonucleoside hydrolase 1 (pyrimidine-specific))

EC Number:

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 in which it was curated.

The reaction is physiologically favored in the direction shown.

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

Kinetic Parameters:

Km (μM)

Enzymatic reaction of: cytidine nucleosidase (ribonucleoside hydrolase 1 (pyrimidine-specific))

EC Number:

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 direction in which it was curated.

The reaction is irreversible in the direction shown.

In Pathways: pyrimidine ribonucleosides salvage III

Kinetic Parameters:

Km (μM)

Sequence Features

Protein sequence of ribonucleoside hydrolase 1 (pyrimidine-specific) with features indicated

Feature Class Location Citations Comment
Active-Site 240
UniProt: Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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

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

Garau10: Garau G, Muzzolini L, Tornaghi P, Degano M (2010). "Active site plasticity revealed from the structure of the enterobacterial N-ribohydrolase RihA bound to a competitive inhibitor." BMC Struct Biol 10;14. PMID: 20529317

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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."

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

Muzzolini06: Muzzolini L, Versees W, Tornaghi P, Van Holsbeke E, Steyaert J, Degano M (2006). "New insights into the mechanism of nucleoside hydrolases from the crystal structure of the Escherichia coli YbeK protein bound to the reaction product." Biochemistry 45(3);773-82. PMID: 16411753

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."

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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 Sun Oct 4, 2015, biocyc13.