Escherichia coli K-12 substr. MG1655 Enzyme: ribose-5-phosphate isomerase A

Gene: rpiA Accession Numbers: EG11443 (EcoCyc), b2914, ECK2910

Synonyms: ygfC

Regulation Summary Diagram: ?

Regulation summary diagram for rpiA

Subunit composition of ribose-5-phosphate isomerase A = [RpiA]2
         ribose-5-phosphate isomerase A = RpiA

There are two physically and genetically distinct ribose-5-phosphate isomerases present in E. coli [David70, Skinner71]. The constitutive ribose-5-phosphate isomerase A (RpiA) normally accounts for more than 99% of the ribose-5-phosphate isomerase activity in the cell and functions in the pentose phosphate pathway (non-oxidative branch) [Skinner71]. The inducible ribose-5-phosphate isomerase B can substitute for RpiA's function if its expression is induced [Skinner74, Sorensen96]. There is no sequence similarity between the two enzymes [Sorensen96].

Crystal structures of RpiA have been solved and active site residues and an acid-base catalytic mechanism were predicted [Rangarajan02, Zhang03b].

An rpiA mutant requires ribose for growth [Skinner71, Sorensen96].

RpiA: "ribosephosphate isomerase A" [Skinner74]

Review: [Sprenger95b]

Citations: [Edwards00, Wang06b]

Locations: cytosol

Map Position: [3,056,688 <- 3,057,347] (65.88 centisomes, 237°)
Length: 660 bp / 219 aa

Molecular Weight of Polypeptide: 22.86 kD (from nucleotide sequence), 27.0 kD (experimental) [HoveJensen93 ]

Molecular Weight of Multimer: 45.0 kD (experimental) [Essenberg75a]

Isozyme Sequence Similarity:
allose-6-phosphate isomerase / ribose-5-phosphate isomerase B monomer: NO

Unification Links: ASAP:ABE-0009567 , CGSC:264 , DIP:DIP-10739N , EchoBASE:EB1413 , EcoGene:EG11443 , EcoliWiki:b2914 , ModBase:P0A7Z0 , OU-Microarray:b2914 , PortEco:rpiA , PR:PRO_000023806 , Pride:P0A7Z0 , Protein Model Portal:P0A7Z0 , RefSeq:NP_417389 , RegulonDB:EG11443 , SMR:P0A7Z0 , String:511145.b2914 , UniProt:P0A7Z0

Relationship Links: InterPro:IN-FAMILY:IPR004788 , InterPro:IN-FAMILY:IPR020672 , Panther:IN-FAMILY:PTHR11934 , PDB:Structure:1KS2 , PDB:Structure:1LKZ , PDB:Structure:1O8B , Pfam:IN-FAMILY:PF06026

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006014 - D-ribose metabolic process Inferred from experiment [Skinner71]
GO:0006098 - pentose-phosphate shunt Inferred by computational analysis [UniProtGOA12]
GO:0009052 - pentose-phosphate shunt, non-oxidative branch Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0004751 - ribose-5-phosphate isomerase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Essenberg75a, HoveJensen93]
GO:0042803 - protein homodimerization activity Inferred from experiment [Essenberg75a]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05, Lasserre06]

MultiFun Terms: metabolism carbon utilization carbon compounds
metabolism central intermediary metabolism non-oxidative branch, pentose pathway

Essentiality data for rpiA 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]
Yes [Feist07, Comment 3]

Last-Curated ? 15-Jul-2011 by Keseler I , SRI International

Enzymatic reaction of: ribose-5-phosphate isomerase A

Synonyms: phosphopentosisomerase, phosphoriboisomerase, ribose-P isomerase A, D-ribose-5-phosphate ketol-isomerase

EC Number:

D-ribose 5-phosphate <=> D-ribulose 5-phosphate

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.

In Pathways: pentose phosphate pathway , pentose phosphate pathway (non-oxidative branch)

Inhibitors (Unknown Mechanism): D-arabinose 5-phosphate [Zhang03b] , AMP [Essenberg75a]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
D-ribose 5-phosphate
830.0, 4400.0
[Essenberg75a, BRENDA14]
D-ribose 5-phosphate
[Zhang03b, BRENDA14]

Sequence Features

Protein sequence of ribose-5-phosphate isomerase A with features indicated

Feature Class Location Citations Comment
Protein-Segment 28 -> 31
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 81
[Zhang03b, UniProt14]
UniProt: Catalytic efficiency decreases by 10,000-fold, with no measurable effect on affinity binding.
Protein-Segment 81 -> 84
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 84
[Zhang03b, UniProt14]
UniProt: Activity decreases by 250-fold, with little change on affinity binding.
Mutagenesis-Variant 94
[Zhang03b, UniProt14]
UniProt: Has a 1500-fold lower Catalytic efficiency than the wild-type, but affinity binding is increased by a factor of seven.
Protein-Segment 94 -> 97
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Active-Site 103
[Zhang03b, UniProt14]
UniProt: Proton acceptor.
Amino-Acid-Sites-That-Bind 121
UniProt: Substrate.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b2914 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11443; 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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

David70: David J, Wiesmeyer H (1970). "Regulation of ribose metabolism in Escherichia coli. II. Evidence for two ribose-5-phosphate isomerase activities." Biochim Biophys Acta 208(1);56-67. PMID: 4909663

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

Edwards00: Edwards JS, Palsson BO (2000). "Robustness analysis of the Escherichia coli metabolic network." Biotechnol Prog 16(6);927-39. PMID: 11101318

Essenberg75a: Essenberg MK, Cooper RA (1975). "Two ribose-5-phosphate isomerases from Escherichia coli K-12: partial chacterisation of the enzymes and consideration of their possible physiological roles." Eur J Biochem 1975;55:323-332. PMID: 1104357

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

HoveJensen93: Hove-Jensen B, Maigaard M (1993). "Escherichia coli rpiA gene encoding ribose phosphate isomerase A." J Bacteriol 1993;175(17);5628-35. PMID: 8366047

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

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Rangarajan02: Rangarajan ES, Sivaraman J, Matte A, Cygler M (2002). "Crystal structure of D-ribose-5-phosphate isomerase (RpiA) from Escherichia coli." Proteins 48(4);737-40. PMID: 12211039

Skinner71: Skinner AJ, Cooper RA (1971). "The regulation of ribose-5-phosphate isomerisation in Escherichia coli K12." FEBS Lett 12(5);293-296. PMID: 11945603

Skinner74: Skinner AJ, Cooper RA (1974). "Genetic studies on ribose 5-phosphate isomerase mutants of Escherichia coli K-12." J Bacteriol 118(3);1183-5. PMID: 4598000

Sorensen96: Sorensen KI, Hove-Jensen B (1996). "Ribose catabolism of Escherichia coli: characterization of the rpiB gene encoding ribose phosphate isomerase B and of the rpiR gene, which is involved in regulation of rpiB expression." J Bacteriol 1996;178(4);1003-11. PMID: 8576032

Sprenger95b: Sprenger GA (1995). "Genetics of pentose-phosphate pathway enzymes of Escherichia coli K-12." Arch Microbiol 1995;164(5);324-30. PMID: 8572885

UniProt14: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-14 00:00:00." Database.

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

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

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

Wang06b: Wang Z, Xiang L, Shao J, Wegrzyn A, Wegrzyn G (2006). "Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism." Microb Cell Fact 5;34. PMID: 17112383

Zhang03b: Zhang R, Andersson CE, Savchenko A, Skarina T, Evdokimova E, Beasley S, Arrowsmith CH, Edwards AM, Joachimiak A, Mowbray SL (2003). "Structure of Escherichia coli ribose-5-phosphate isomerase: a ubiquitous enzyme of the pentose phosphate pathway and the Calvin cycle." Structure 11(1);31-42. PMID: 12517338

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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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