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Escherichia coli K-12 substr. MG1655 Enzyme: fused diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase



Gene: ribD Accession Numbers: EG11321 (EcoCyc), b0414, ECK0408

Synonyms: nusII, ribG, ybaE

Regulation Summary Diagram: ?

Subunit composition of fused diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase = [RibD]2
         fused diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase = RibD

Summary:
The ribD gene encodes a bifunctional enzyme that catalyzes the second (deamination) and third (reduction) steps in the riboflavin biosynthesis pathway. The N-terminal domain encodes the deaminase activity, and the C-terminal domain encodes the reductase activity [Richter97]. The deaminase domain shows structural similarity to the cytidine deaminase superfamily of enzymes [Magalhaes08].

The kcat of the reduction reaction, 19 min-1, is 20 times slower than the kcat of the deamination reaction, 370 min-1, suggesting that there is no channeling of the substrate and no kinetic coupling between the two active sites [Magalhaes08]. A kinetic mechanism similar to that of dihydrofolate reductase has been proposed [Magalhaes08].

The enzyme is a dimer in solution. Crystal structures of RibD alone and in complex with the oxidized cosubstrate NADP+ or the substrate analog ribose-5-phosphate have been solved [Stenmark07].

ribD is an essential gene [Baba06].

Gene Citations: [Torrents07]

Locations: cytosol

Map Position: [432,679 -> 433,782] (9.33 centisomes)
Length: 1104 bp / 367 aa

Molecular Weight of Polypeptide: 40.338 kD (from nucleotide sequence), 40 kD (experimental) [Richter97 ]

pI: 7.68

Unification Links: ASAP:ABE-0001441 , CGSC:35685 , DIP:DIP-10708N , EchoBASE:EB1297 , EcoGene:EG11321 , EcoliWiki:b0414 , Mint:MINT-1221612 , ModBase:P25539 , OU-Microarray:b0414 , PortEco:ribD , PR:PRO_000023752 , Pride:P25539 , Protein Model Portal:P25539 , RefSeq:NP_414948 , RegulonDB:EG11321 , SMR:P25539 , String:511145.b0414 , UniProt:P25539

Relationship Links: InterPro:IN-FAMILY:IPR002125 , InterPro:IN-FAMILY:IPR002734 , InterPro:IN-FAMILY:IPR004794 , InterPro:IN-FAMILY:IPR011549 , InterPro:IN-FAMILY:IPR016192 , InterPro:IN-FAMILY:IPR016193 , InterPro:IN-FAMILY:IPR024072 , PDB:Structure:2G6V , PDB:Structure:2O7P , PDB:Structure:2OBC , Pfam:IN-FAMILY:PF00383 , Pfam:IN-FAMILY:PF01872 , Prosite:IN-FAMILY:PS00903

In Paralogous Gene Group: 431 (2 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0009231 - riboflavin biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA01a, Magalhaes08]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0008703 - 5-amino-6-(5-phosphoribosylamino)uracil reductase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Richter97, Magalhaes08]
GO:0008835 - diaminohydroxyphosphoribosylaminopyrimidine deaminase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Richter97, Magalhaes08]
GO:0050661 - NADP binding Inferred from experiment Inferred by computational analysis [GOA01a, Magalhaes08]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0008270 - zinc ion binding Inferred by computational analysis [GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers riboflavin

Essentiality data for ribD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Credits:
Created 28-Dec-2007 by Keseler I , SRI International
Last-Curated ? 06-Jun-2008 by Keseler I , SRI International


Enzymatic reaction of: diaminohydroxyphosphoribosylaminopyrimidine deaminase

Synonyms: riboflavin specific deaminase

EC Number: 3.5.4.26

2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one + H+ + H2O <=> 5-amino-6-(5-phospho-D-ribosylamino)uracil + ammonium

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: flavin biosynthesis I (bacteria and plants)

Summary:
The enzyme was fist partially purified from E. coli B [Burrows78].

Kinetic Parameters:

Substrate
Km (μM)
Citations
2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one
1300.0
[Magalhaes08]


Enzymatic reaction of: 5-amino-6-(5-phosphoribosylamino)uracil reductase

EC Number: 1.1.1.193

5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH + H+ <=> 5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP+

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 NADPH: NADH [Richter97 ]

In Pathways: flavin biosynthesis I (bacteria and plants)

Summary:
The enzyme was fist partially purified from E. coli B [Burrows78].

Earlier experiments indicated that the enzyme has approximately equal activity using NADPH or NADH as substrates [Richter97], while recent studies showed that NADH is a poor substrate [Magalhaes08].

Inhibitors (Competitive): isoniazid-NADP [Magalhaes08]

Inhibitors (Uncompetitive): isoniazid-NADP [Magalhaes08]

Kinetic Parameters:

Substrate
Km (μM)
Citations
5-amino-6-(5-phospho-D-ribosylamino)uracil
37.0
[Magalhaes08]
NADPH
20.0
[Magalhaes08]


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 1 -> 145
[UniProt10a]
UniProt: Deaminase; Sequence Annotation Type: region of interest;
Metal-Binding-Site 50
[UniProt10a]
UniProt: Zinc; catalytic; Non-Experimental Qualifier: by similarity;
Active-Site 52
[UniProt10a]
UniProt: Proton donor; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 75
[UniProt10a]
UniProt: Zinc; catalytic; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 84
[UniProt10a]
UniProt: Zinc; catalytic; Non-Experimental Qualifier: by similarity;
Protein-Segment 146 -> 367
[UniProt10a]
UniProt: Reductase; Sequence Annotation Type: region of interest;
Nucleotide-Phosphate-Binding-Region 161 -> 164
[UniProt10]
UniProt: NADP;
Amino-Acid-Sites-That-Bind 168
[UniProt10]
UniProt: Substrate;
Amino-Acid-Sites-That-Bind 170
[UniProt10]
UniProt: NADP;
Amino-Acid-Sites-That-Bind 184
[UniProt10]
UniProt: Substrate;
Amino-Acid-Sites-That-Bind 196
[UniProt10]
UniProt: NADP;
Amino-Acid-Sites-That-Bind 200
[UniProt10]
UniProt: NADP;
Amino-Acid-Sites-That-Bind 204
[UniProt10]
UniProt: Substrate; via amide nitrogen;
Amino-Acid-Sites-That-Bind 207
[UniProt10]
UniProt: Substrate;
Amino-Acid-Sites-That-Bind 234
[UniProt10]
UniProt: NADP;
Amino-Acid-Sites-That-Bind 299
[UniProt10]
UniProt: Substrate;
Nucleotide-Phosphate-Binding-Region 301 -> 304
[UniProt10]
UniProt: NADP;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0414 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11321; 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

Burrows78: Burrows RB, Brown GM (1978). "Presence of Escherichia coli of a deaminase and a reductase involved in biosynthesis of riboflavin." J Bacteriol 1978;136(2);657-67. PMID: 30756

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

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Magalhaes08: Magalhaes ML, Argyrou A, Cahill SM, Blanchard JS (2008). "Kinetic and mechanistic analysis of the Escherichia coli ribD-encoded bifunctional deaminase-reductase involved in riboflavin biosynthesis." Biochemistry 47(24);6499-507. PMID: 18500821

Richter97: Richter G, Fischer M, Krieger C, Eberhardt S, Luttgen H, Gerstenschlager I, Bacher A (1997). "Biosynthesis of riboflavin: characterization of the bifunctional deaminase-reductase of Escherichia coli and Bacillus subtilis." J Bacteriol 179(6);2022-8. PMID: 9068650

Stenmark07: Stenmark P, Moche M, Gurmu D, Nordlund P (2007). "The crystal structure of the bifunctional deaminase/reductase RibD of the riboflavin biosynthetic pathway in Escherichia coli: implications for the reductive mechanism." J Mol Biol 373(1);48-64. PMID: 17765262

Torrents07: Torrents E, Grinberg I, Gorovitz-Harris B, Lundstrom H, Borovok I, Aharonowitz Y, Sjoberg BM, Cohen G (2007). "NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes." J Bacteriol 189(14);5012-21. PMID: 17496099

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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."

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


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 Fri Dec 19, 2014, BIOCYC14A.