Escherichia coli K-12 substr. MG1655 Enzyme: ribose pyranase

Gene: rbsD Accession Numbers: EG10817 (EcoCyc), b3748, ECK3742

Synonyms: rbsP

Regulation Summary Diagram: ?

Regulation summary diagram for rbsD

Subunit composition of ribose pyranase = [RbsD]10
         ribose pyranase = RbsD

RbsD is a ribose pyranase; it binds specifically to the β-furan and β-pyran forms of ribose and increases the exchange rate between the two forms [Ryu04].

The RbsD protein is required for efficient utilization of ribose when ribose is transported into the cell via a mutated form of PtsG, the glucose transporter. A mutation in rbsD does not abolish ribose transport [Oh99]. An rbsD point mutant that abolishes pyranase activity is impaired in the utilization of D-ribose as a source of carbon and energy [Ryu04].

A preliminary crystallographic analysis of RbsD has been reported, but no structure coordinates have been deposited with PDB [Kim01c]. Based on analytical centrifugation analysis, RbsD was initially reported to be an octamer in solution [Kim01c]; analysis of the crystal structure showed it to be a decamer, similar to the Bacillus subtilis homolog [Kim03a], while gel permeation chromatography indicated that the protein was a heptamer [Ryu04]. Under urea-induced denaturation conditions, the homodecamer undergoes stepwise disassembly and non-stepwise reassembly [Feng06, Feng09].

Overproduction of RbsD inhibits growth on D-ribose due to accumulation of methylglyoxal [Kim04c].

Citations: [Lease98]

Gene Citations: [Bell86, Burland93]

Locations: cytosol

Map Position: [3,931,374 -> 3,931,793] (84.73 centisomes, 305°)
Length: 420 bp / 139 aa

Molecular Weight of Polypeptide: 15.292 kD (from nucleotide sequence)

Molecular Weight of Multimer: 150.0 kD (experimental) [Feng06]

Unification Links: ASAP:ABE-0012256 , CGSC:314 , EchoBASE:EB0810 , EcoGene:EG10817 , EcoliWiki:b3748 , ModBase:P04982 , OU-Microarray:b3748 , PortEco:rbsD , PR:PRO_000023685 , Protein Model Portal:P04982 , RefSeq:NP_418204 , RegulonDB:EG10817 , SMR:P04982 , String:511145.b3748 , UniProt:P04982

Relationship Links: InterPro:IN-FAMILY:IPR007721 , InterPro:IN-FAMILY:IPR023064 , InterPro:IN-FAMILY:IPR023750 , Pfam:IN-FAMILY:PF05025

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for rbsD

GO Terms:

Biological Process: GO:0019303 - D-ribose catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, GOA06, Ryu04]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0005996 - monosaccharide metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0016866 - intramolecular transferase activity Inferred from experiment [Ryu04]
GO:0042802 - identical protein binding Inferred from experiment [Feng06]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016872 - intramolecular lyase activity Inferred by computational analysis [GOA06, GOA01]
GO:0048029 - monosaccharide binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for rbsD 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 05-Nov-2007 by Keseler I , SRI International
Last-Curated ? 29-Jan-2014 by Keseler I , SRI International

Enzymatic reaction of: ribose pyranase

Synonyms: D-ribose pyranase

EC Number:

β-D-ribopyranose <=> β-D-ribofuranose

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

This reaction is reversible.

Alternative Substrates for β-D-ribopyranose: D-allose [Ryu04 ]

In Pathways: ribose degradation

Sequence Features

Protein sequence of ribose pyranase with features indicated

Feature Class Location Citations Comment
Mutagenesis-Variant 20
[Ryu04, UniProt11]
UniProt: Loss of pyranase activity.
Active-Site 20
UniProt: Proton donor; Non-Experimental Qualifier: probable;
Amino-Acid-Sites-That-Bind 28
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 106
[Ryu04, UniProt11]
UniProt: Retains one-third of the original activity.
Amino-Acid-Sites-That-Bind 106
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Protein-Segment 128 -> 130
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b3748 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10817; 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

Bell86: Bell AW, Buckel SD, Groarke JM, Hope JN, Kingsley DH, Hermodson MA (1986). "The nucleotide sequences of the rbsD, rbsA, and rbsC genes of Escherichia coli K12." J Biol Chem 261(17);7652-8. PMID: 3011793

Burland93: Burland V, Plunkett G, Daniels DL, Blattner FR (1993). "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication." Genomics 1993;16(3);551-61. PMID: 7686882

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

Feng06: Feng Y, Jiao W, Fu X, Chang Z (2006). "Stepwise disassembly and apparent nonstepwise reassembly for the oligomeric RbsD protein." Protein Sci 15(6);1441-8. PMID: 16731978

Feng09: Feng Y, Zhang M, Hu M, Zheng J, Jiao W, Chang Z (2009). "Disassembly intermediates of RbsD protein remain oligomeric despite the loss of an intact secondary structure." Sci China C Life Sci 52(11);997-1002. PMID: 19937196

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

GOA01: 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."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Kim01c: Kim MS, Oh H, Park C, Oh BH (2001). "Crystallization and preliminary X-ray crystallographic analysis of Escherichia coli RbsD, a component of the ribose-transport system with unknown biochemical function." Acta Crystallogr D Biol Crystallogr 57(Pt 5);728-30. PMID: 11320319

Kim03a: Kim MS, Shin J, Lee W, Lee HS, Oh BH (2003). "Crystal structures of RbsD leading to the identification of cytoplasmic sugar-binding proteins with a novel folding architecture." J Biol Chem 278(30);28173-80. PMID: 12738765

Kim04c: Kim I, Kim E, Yoo S, Shin D, Min B, Song J, Park C (2004). "Ribose utilization with an excess of mutarotase causes cell death due to accumulation of methylglyoxal." J Bacteriol 186(21);7229-35. PMID: 15489434

Lease98: Lease RA, Cusick ME, Belfort M (1998). "Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci." Proc Natl Acad Sci U S A 95(21);12456-61. PMID: 9770507

Oh99: Oh H, Park Y, Park C (1999). "A mutated PtsG, the glucose transporter, allows uptake of D-ribose." J Biol Chem 274(20);14006-11. PMID: 10318813

Ryu04: Ryu KS, Kim C, Kim I, Yoo S, Choi BS, Park C (2004). "NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration." J Biol Chem 279(24);25544-8. PMID: 15060078

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

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

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

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Other References Related to Gene Regulation

Mauzy92: Mauzy CA, Hermodson MA (1992). "Structural and functional analyses of the repressor, RbsR, of the ribose operon of Escherichia coli." Protein Sci 1992;1(7);831-42. PMID: 1304369

Shimada13: Shimada T, Kori A, Ishihama A (2013). "Involvement of the ribose operon repressor RbsR in regulation of purine nucleotide synthesis in Escherichia coli." FEMS Microbiol Lett 344(2);159-65. PMID: 23651393

Zheng04: Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004). "Identification of the CRP regulon using in vitro and in vivo transcriptional profiling." Nucleic Acids Res 32(19);5874-93. PMID: 15520470

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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