print visible entries

print all entries

Ligand 5,6-dimethylbenzimidazole

Basic Ligand Information

Molecular Structure

Pathway Source

Pathways

BRENDA

vitamin B12 metabolism

KEGG

Biosynthesis of cofactors, Porphyrin metabolism, Riboflavin metabolism

MetaCyc

5,6-dimethylbenzimidazole biosynthesis I (aerobic), 5,6-dimethylbenzimidazole biosynthesis II (anaerobic), adenosylcobalamin biosynthesis from adenosylcobinamide-GDP I, bassianin and desmethylbassianin biosynthesis, superpathway of adenosylcobalamin salvage from cobinamide I, superpathway of adenosylcobalamin salvage from cobinamide II more

Show all BRENDA pathways known for 5,6-dimethylbenzimidazole

close all tables

open all tables

Roles as Enzyme Ligand

In Vivo Substrate in Enzyme-catalyzed Reactions (7 results)

top print hide

Show Natural Substrate (7 entries)

EC NUMBER

PROVEN IN VIVO REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

2.4.2.21

beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + alpha-ribazole 5'-phosphate

759786, 736750

1d0s, 3D-view

2.4.2.21

beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + alpha-ribazole 5'-phosphate

759786, 736750

4hdr, 3D-view

2.4.2.21

beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + alpha-ribazole 5'-phosphate

759786, 736750

4kqg, 3D-view

2.4.2.21

NAD+ + 5,6-dimethylbenzimidazole = nicotinamide + alpha-5,6-dimethylbenzimidazole adenine dinucleotide

662777

1d0s, 3D-view

2.4.2.21

NAD+ + 5,6-dimethylbenzimidazole = nicotinamide + alpha-5,6-dimethylbenzimidazole adenine dinucleotide

662777

4hdr, 3D-view

2.4.2.21

NAD+ + 5,6-dimethylbenzimidazole = nicotinamide + alpha-5,6-dimethylbenzimidazole adenine dinucleotide

662777

4kqg, 3D-view

2.4.2.21

6 entries

2.4.2.55

beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + alpha-ribazole 5'-phosphate

723215

-

In Vivo Product in Enzyme-catalyzed Reactions (5 results)

top print hide

Show Natural Product (5 entries)

EC NUMBER

PROVEN IN VIVO REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

1.13.11.79

FMNH2 + NADH + H+ + O2 + alloxan = 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + NAD+ + dialuric acid

0

-

1.13.11.79

FMNH2 + NADH + H+ + O2 = 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + NAD+ + ?

0

-

1.13.11.79

FMNH2 + O2 = 5,6-dimethylbenzimidazole + ?

0

-

1.13.11.79

FMNH2 + O2 = 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + dialiric acid + pyrimidinetrione + alloxan

0

-

1.13.11.79

FMNH2 + O2 = 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + urea + ?

0

-

1.13.11.79

5 entries

Substrate in Enzyme-catalyzed Reactions (18 results)

top print hide

Show Substrate (18 entries)

EC NUMBER

REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

2.4.2.21

5,6-dimethylbenzimidazole + beta-nicotinate D-ribonucleotide = nicotinate + N1-(5-phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole

721677, 723215

1d0s, 3D-view

2.4.2.21

5,6-dimethylbenzimidazole + beta-nicotinate D-ribonucleotide = nicotinate + N1-(5-phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole

721677, 723215

4hdr, 3D-view

2.4.2.21

5,6-dimethylbenzimidazole + beta-nicotinate D-ribonucleotide = nicotinate + N1-(5-phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole

721677, 723215

4kqg, 3D-view

2.4.2.21

beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + alpha-ribazole 5'-phosphate

735682, 735924, 759786, 736750

1d0s, 3D-view

2.4.2.21

beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + alpha-ribazole 5'-phosphate

735682, 735924, 759786, 736750

4hdr, 3D-view

2.4.2.21

beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + alpha-ribazole 5'-phosphate

735682, 735924, 759786, 736750

4kqg, 3D-view

2.4.2.21

beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + N1-(5-phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole

489780, 662777, 489776, 489777, 489778, 489779, 704323

1d0s, 3D-view

2.4.2.21

beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + N1-(5-phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole

489780, 662777, 489776, 489777, 489778, 489779, 704323

4hdr, 3D-view

2.4.2.21

beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + N1-(5-phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole

489780, 662777, 489776, 489777, 489778, 489779, 704323

4kqg, 3D-view

2.4.2.21

NAD+ + 5,6-dimethylbenzimidazole = nicotinamide + alpha-5,6-dimethylbenzimidazole adenine dinucleotide

662777

1d0s, 3D-view

2.4.2.21

NAD+ + 5,6-dimethylbenzimidazole = nicotinamide + alpha-5,6-dimethylbenzimidazole adenine dinucleotide

662777

4hdr, 3D-view

2.4.2.21

NAD+ + 5,6-dimethylbenzimidazole = nicotinamide + alpha-5,6-dimethylbenzimidazole adenine dinucleotide

662777

4kqg, 3D-view

2.4.2.21

NMN + 5,6-dimethylbenzimidazole = nicotinamide + ?

662777

1d0s, 3D-view

2.4.2.21

NMN + 5,6-dimethylbenzimidazole = nicotinamide + ?

662777

4hdr, 3D-view

2.4.2.21

NMN + 5,6-dimethylbenzimidazole = nicotinamide + ?

662777

4kqg, 3D-view

2.4.2.21

15 entries

2.4.2.55

beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + alpha-ribazole 5'-phosphate

723215

-

2.4.2.6

thymidine + 5,6-dimethyl-benzimidazole = thymine + ?

638043

-

6.3.5.9

DMB + nicotinic acid mononucleotide = DMB-ribose-5'-phosphate

651627

-

Product in Enzyme-catalyzed Reactions (9 results)

top print hide

Show Product (9 entries)

EC NUMBER

REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

1.13.11.79

FMNH2 + NADH + H+ + O2 + alloxan = 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + NAD+ + dialuric acid

0

-

1.13.11.79

FMNH2 + NADH + H+ + O2 + H2O = 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + NAD+ + ?

0

-

1.13.11.79

FMNH2 + NADH + H+ + O2 = 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + NAD+ + ?

0

-

1.13.11.79

FMNH2 + NADPH + H+ + O2 = 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + NADP+ + ?

0

-

1.13.11.79

FMNH2 + O2 = 5,6-dimethylbenzimidazole + ?

0

-

1.13.11.79

FMNH2 + O2 = 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + dialiric acid + pyrimidinetrione + alloxan

0

-

1.13.11.79

FMNH2 + O2 = 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + other product(s)

0

-

1.13.11.79

FMNH2 + O2 = 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + urea + ?

0

-

1.13.11.79

8 entries

3.2.2.1

5,6-dimethyl-1-beta-D-ribofuranosylbenzimidazole + H2O = 5,6-dimethylbenzimidazole + D-ribose

0

-

Inhibitor in Enzyme-catalyzed Reactions (1 result)

top print hide

Show Inhibitors (1 entry)

EC NUMBER

COMMENTARY

LITERATURE

ENZYME 3D STRUCTURE

1.17.3.2

poor inhibitor

685516

-

3D Structure of Enzyme-Ligand-Complex (PDB) (15 results)

top print hide

Show 3D Structure of Enzyme-Ligand-Complex (PDB) (15 entries)

EC NUMBER

ENZYME 3D STRUCTURE

2.4.2.21

1d0s, 3D-view

2.4.2.21

4hdr, 3D-view

2.4.2.21

4kqg, 3D-view

2.4.2.21

1d0s, 3D-view

2.4.2.21

4hdr, 3D-view

2.4.2.21

4kqg, 3D-view

2.4.2.21

1d0s, 3D-view

2.4.2.21

4hdr, 3D-view

2.4.2.21

4kqg, 3D-view

2.4.2.21

1d0s, 3D-view

2.4.2.21

4hdr, 3D-view

2.4.2.21

4kqg, 3D-view

2.4.2.21

1d0s, 3D-view

2.4.2.21

4hdr, 3D-view

2.4.2.21

4kqg, 3D-view

2.4.2.21

15 entries

Enzyme Kinetic Parameters

k_cat Value (Turnover Number) (1 result)

top print hide

Show Turnover Number (1 entry)

EC NUMBER

TURNOVER NUMBER [1/S]

TURNOVER NUMBER MAXIMUM [1/S]

COMMENTARY

LITERATURE

2.4.2.21

1.6

-

pH 9.0, 37°C, wild-type

721677

K_M Value (3 results)

top print hide

Show KM Value (3 entries)

EC NUMBER

KM VALUE [MM]

KM VALUE MAXIMUM [MM]

COMMENTARY

LITERATURE

2.4.2.21

0.000016

-

-

489779

2.4.2.21

0.01

-

or less

489780

2.4.2.21

0.415

-

pH 9.0, 37°C, wild-type

721677

2.4.2.21

3 entries

References & Links

Literature References (16)

top print hide

Show Reference (16 entries)

BRENDA REFERENCE ID

PUBMED ID

TITLE

YEAR

AUTHORS

JOURNAL

VOLUME

PAGES

489776

14253445

Partial purification and properties of a single displacement trans-N-glycoside

1965

Friedmann, H.C.

J. Biol. Chem.

240

413-418

489777

4238408

Vitamin B 12 biosynthesis. Enzyme studies on the formation of the alpha-glycosidic nucleotide precursor

1969

Fyfe, J.A.; Friedmann, H.C.

J. Biol. Chem.

244

1659-1666

489778

5780835

Pseudovitamin B 12 biosynthesis. Enzymatic formation of a new adenylic acid, 7-alpha-D-ribofuranosyladenine 5-phosphate

1969

Friedmann, H.C.; Fyfe, J.A.

J. Biol. Chem.

244

1667-1671

489779

1917841

Genetic analysis, nucleotide sequence, and products of two Pseudomonas denitrificans cob genes encoding nicotinate-nucleotide: dimethylbenzimidazole phosphoribosyltransferase and cobalamin (5-phosphate) synthase

1991

Cameron, B.; Blanche, F.; Rouyez, M.C.; Bisch, D.; Famechon, A.; Couder, M.; Cauchois, L.; Thibaut, D.; Debussche, L.; Crouzet, J.

J. Bacteriol.

173

6066-6073

489780

9211916

Purification and characterization of CobT, the nicotinate-mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase enzyme from Salmonella typhimurium LT2

1997

Trzebiatowski, J.R.; Escalante-Semerena, J.C.

J. Biol. Chem.

272

17662-17667

638043

1175597

trans-N-Deoxyribosylase: substrate specificity studies. Purine bases as acceptors

1975

Holguin, J.; Cardinaud, R.

Eur. J. Biochem.

54

515-520

651627

8955330

cobB function is required for catabolism of propionate in Salmonella typhimurium LT2: evidence for existence of a substitute function for CobB within the 1,2-propanediol utilization (pdu) operon

1996

Tsang, A.W.; Escalante-Semerena, J.C.

J. Bacteriol.

178

7016-7019

662777

12686640

alpha-5,6-Dimethylbenzimidazole adenine dinucleotide (alpha-DAD), a putative new intermediate of coenzyme B12 biosynthesis in Salmonella typhimurium

2003

Maggio-Hall, L.A.; Escalante-Semerena, J.C.

Microbiology

149

983-990

685516

17379526

The screening and characterization of 6-aminopurine-based xanthine oxidase inhibitors

2007

Hsieh, J.F.; Wu, S.H.; Yang, Y.L.; Choong, K.F.; Chen, S.T.

Bioorg. Med. Chem.

15

3450-3456

704323

19880598

Functional analysis of the nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) enzyme, involved in the late steps of coenzyme B12 biosynthesis in Salmonella enterica

2010

Claas, K.R.; Parrish, J.R.; Maggio-Hall, L.A.; Escalante-Semerena, J.C.

J. Bacteriol.

192

145-154

721677

23039029

Structural Insights into the Function of the Nicotinate Mononucleotide:phenol/p-cresol Phosphoribosyltransferase (ArsAB) Enzyme from Sporomusa ovata

2012

Newmister, S.A.; Chan, C.H.; Escalante-Semerena, J.C.; Rayment, I.

Biochemistry

51

8571-8582

723215

21696461

ArsAB, a novel enzyme from Sporomusa ovata activates phenolic bases for adenosylcobamide biosynthesis

2011

Chan, C.H.; Escalante-Semerena, J.C.

Mol. Microbiol.

81

952-967

735682

25412146

Regiospecific formation of cobamide isomers is directed by CobT

2014

Crofts, T.S.; Hazra, A.B.; Tran, J.L.; Sokolovskaya, O.M.; Osadchiy, V.; Ad, O.; Pelton, J.; Bauer, S.; Taga, M.E.

Biochemistry

53

7805-7815

735924

24055007

Cobamide structure depends on both lower ligand availability and CobT substrate specificity

2013

Crofts, T.S.; Seth, E.C.; Hazra, A.B.; Taga, M.E.

Chem. Biol.

20

1265-1274

736750

26597297

BluB/CobT2 fusion enzyme activity reveals mechanisms responsible for production of active form of vitamin B12 by Propionibacterium freudenreichii

2015

Deptula, P.; Kylli, P.; Chamlagain, B.; Holm, L.; Kostiainen, R.; Piironen, V.; Savijoki, K.; Varmanen, P.

Microb. Cell Fact.

14

186

759786

27748967

Salmonella enterica synthesizes 5,6-dimethylbenzimidazolyl-(DMB)-alpha-riboside. Why some Firmicutes do not require the canonical DMB activation system to synthesize adenosylcobalamin

2017

Mattes, T.; Escalante-Semerena, J.

Mol. Microbiol.

103

269-281

Links to other databases for 5,6-dimethylbenzimidazole

top print hide

Show Links (1 entry)

ChEBI

PubChem