Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015 (Sat)
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015 (Sat)
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015 (Sat)
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015 (Sat)
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015 (Sat)
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: 1,4-dihydroxy-2-naphthoyl-CoA synthase



Gene: menB Accession Numbers: EG11368 (EcoCyc), b2262, ECK2256

Regulation Summary Diagram: ?

Regulation summary diagram for menB

Subunit composition of 1,4-dihydroxy-2-naphthoyl-CoA synthase = [MenB]6

Summary:
1,4-Dihydroxy-2-naphthoyl-CoA synthase catalyzes a major step in menaquinone biosynthesis, formation of the bicyclic ring system by an intramolecular Claisen condensation [Heide82, Sharma92].

The enzyme requires a bound bicarbonate ion for full activity, and the crystal structure of the Salmonella enterica ortholog contains a bicarbonate ion. Both the S. enterica and the E. coli enzymes contain a glycine residue in the position corresponding to the essential active site Asp185 residue of the Mycobacterium tuberculosis enzyme, and the bicarbonate ion is found close to this Gly156 residue. Site-directed mutagenesis showed that Gly156 is essential for catalytic activity [Jiang10]. Asp163 interacts with the C1 hydroxyl group of DHNA-CoA; a D163A mutation abolishes activity as well as ligand binding [Chen11b]. A Y97F mutant lacks catalytic activity [Li11a]. Reaction mechanisms have been proposed [Jiang10, Chen11b, Li11a].

A crystal structure of MenB with bound O-succinylbenzoyl-aminoCoA (OSB-NCoA), a stable substrate analog, has been solved at 2 Å resolution. The structure reveals the position of all active site residues and supports a mechanism involving the direct participation of the two conserved Tyr residues Y97 and Y258 in the intramolecular transfer of the substrate proton to the benzylic carboxylate of the substrate [Li11a].

Gene Citations: [Sharma96]

Locations: cytosol

Map Position: [2,373,984 <- 2,374,841] (51.17 centisomes, 184°)
Length: 858 bp / 285 aa

Molecular Weight of Polypeptide: 31.633 kD (from nucleotide sequence)

pI: 6.37

Unification Links: ASAP:ABE-0007476 , CGSC:519 , DIP:DIP-47854N , EchoBASE:EB1342 , EcoGene:EG11368 , EcoliWiki:b2262 , Mint:MINT-1227416 , ModBase:P0ABU0 , OU-Microarray:b2262 , PortEco:menB , PR:PRO_000023201 , Pride:P0ABU0 , Protein Model Portal:P0ABU0 , RefSeq:NP_416765 , RegulonDB:EG11368 , SMR:P0ABU0 , String:511145.b2262 , Swiss-Model:P0ABU0 , UniProt:P0ABU0

Relationship Links: InterPro:IN-FAMILY:IPR001753 , InterPro:IN-FAMILY:IPR010198 , InterPro:IN-FAMILY:IPR014748 , InterPro:IN-FAMILY:IPR018376 , InterPro:IN-FAMILY:IPR029045 , PDB:Structure:3T88 , PDB:Structure:3T89 , PDB:Structure:4ELS , PDB:Structure:4ELW , PDB:Structure:4ELX , PDB:Structure:4I42 , Pfam:IN-FAMILY:PF00378 , Prosite:IN-FAMILY:PS00166

In Paralogous Gene Group: 12 (7 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0009234 - menaquinone biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA06, GOA01a, Young75]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Butland05]
GO:0008935 - 1,4-dihydroxy-2-naphthoyl-CoA synthase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Sharma92, Jiang10, Heide82]
GO:0071890 - bicarbonate binding Inferred from experiment [Jiang10]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers menaquinone, ubiquinone
metabolism energy metabolism, carbon anaerobic respiration

Essentiality data for menB 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]

Credits:
Created 27-Jul-2010 by Keseler I , SRI International
Last-Curated ? 17-Aug-2011 by Keseler I , SRI International


Enzymatic reaction of: 1,4-dihydroxy-2-naphthoyl-CoA synthase

Synonyms: dihydroxynaphthoate synthase, DHNA synthase, o-succinylbenzoyl-CoA 1,4-dihydroxy-2-naphthoate-lyase (cyclizing), naphthoate-CoA synthase, DHNA-CoA synthase

EC Number: 4.1.3.36

4-(2'-carboxyphenyl)-4-oxobutyryl-CoA + H+ <=> 1,4-dihydroxy-2-naphthoyl-CoA + H2O

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 irreversible in the direction shown. [Chen11b]

In Pathways: superpathway of menaquinol-8 biosynthesis I , superpathway of chorismate metabolism , 1,4-dihydroxy-2-naphthoate biosynthesis I

Summary:
Nitrate is a competitive inhibitor with respect to the bicarbonate cofactor [Jiang10].

MenB and DHNA-CoA form a tight complex with a dissociation constant of less than 500 nM [Chen11b].

Cofactors or Prosthetic Groups: hydrogen carbonate [Jiang10]

Inhibitors (Competitive): 1,4-dihydroxy-2-naphthoyl-CoA (Kic = 1.5µM) [Chen11b] , nitrate [Jiang10]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
4-(2'-carboxyphenyl)-4-oxobutyryl-CoA
25.9
0.062, 620.0
0.0024, 23.94
[Li11a, BRENDA14]


Sequence Features

Protein sequence of MenB with features indicated

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 45
[Sun13a, Li11a, UniProt14]
UniProt: Substrate.
Protein-Segment 84 -> 89
[Sun13a, Li11a, UniProt14]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 89
[Sun13a, UniProt14]
UniProt: Strongly decreases affinity for substrate and DHNA-CoA synthase activity.
Mutagenesis-Variant 91
[Sun13a, UniProt14]
UniProt: Loss of DHNA-CoA synthase activity.
Mutagenesis-Variant 97
[Li11a, UniProt14]
UniProt: Loss of DHNA-CoA synthase activity.
Amino-Acid-Sites-That-Bind 97
[Li11a, UniProt14]
UniProt: Substrate.
Protein-Segment 129 -> 133
[Sun13a, Li11a, UniProt11]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Mutagenesis-Variant 154
[Jiang10, UniProt11]
UniProt: Reduces the specific DHNA-CoA synthase activity by 15-fold, whereas its affinity for bicarbonate is reduced by 36-fold.
Protein-Segment 154 -> 156
[Sun12b, UniProt11]
UniProt: Bicarbonate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 155
[Sun13a, Li11a, UniProt15]
UniProt: Substrate.
Mutagenesis-Variant 156
[Li11a, Jiang10, UniProt11]
UniProt: Loss of DHNA-CoA synthase activity.
Amino-Acid-Sites-That-Bind 161
[Sun13a, UniProt15]
UniProt: Substrate.
Mutagenesis-Variant 163
[Chen11b]
D > A mutation causes loss of activity and loss of ligand binding ability [Chen11b].
Mutagenesis-Variant 184
[Jiang10, UniProt11]
UniProt: Reduces the specific DHNA-CoA synthase activity by 530-fold, whereas its affinity for bicarbonate is reduced by 20-fold.
Amino-Acid-Sites-That-Bind 258
[Li11a, UniProt14]
UniProt: Substrate; shared with neighboring subunit.
Mutagenesis-Variant 267
[Sun13a, UniProt14]
UniProt: Strongly decreases affinity for substrate and DHNA-CoA synthase activity.
Mutagenesis-Variant 270
[Sun13a, UniProt14]
UniProt: Strongly decreases affinity for substrate and DHNA-CoA synthase activity.
Mutagenesis-Variant 273
[Sun13a, UniProt14]
UniProt: Impairs protein folding.
Amino-Acid-Sites-That-Bind 273
[Sun13a, Li11a, UniProt14]
UniProt: Substrate; shared with neighboring subunit.


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Notes:

History:
10/20/97 Gene b2262 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11368; 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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Chen11b: Chen M, Jiang M, Sun Y, Guo ZF, Guo Z (2011). "Stabilization of the second oxyanion intermediate by 1,4-dihydroxy-2-naphthoyl-coenzyme A synthase of the menaquinone pathway: spectroscopic evidence of the involvement of a conserved aspartic acid." Biochemistry 50(26);5893-904. PMID: 21627110

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

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."

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

Heide82: Heide L, Arendt S, Leistner E (1982). "Enzymatic synthesis, characterization, and metabolism of the coenzyme A ester of o-succinylbenzoic acid, an intermediate in menaquinone (vitamin K2) biosynthesis." J Biol Chem 1982;257(13);7396-400. PMID: 7045104

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

Jiang10: Jiang M, Chen M, Guo ZF, Guo Z (2010). "A bicarbonate cofactor modulates 1,4-dihydroxy-2-naphthoyl-coenzyme a synthase in menaquinone biosynthesis of Escherichia coli." J Biol Chem 285(39);30159-69. PMID: 20643650

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

Li11a: Li HJ, Li X, Liu N, Zhang H, Truglio JJ, Mishra S, Kisker C, Garcia-Diaz M, Tonge PJ (2011). "Mechanism of the intramolecular Claisen condensation reaction catalyzed by MenB, a crotonase superfamily member." Biochemistry 50(44);9532-44. PMID: 21830810

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

Meganathan81: Meganathan R, Bentley R (1981). "Biosynthesis of o-succinylbenzoic acid in a men- Escherichia coli mutant requires decarboxylation of L-glutamate at the C-1 position." Biochemistry 20(18);5336-40. PMID: 6117313

Sharma92: Sharma V, Suvarna K, Meganathan R, Hudspeth ME (1992). "Menaquinone (vitamin K2) biosynthesis: nucleotide sequence and expression of the menB gene from Escherichia coli." J Bacteriol 1992;174(15);5057-62. PMID: 1629162

Sharma96: Sharma V, Hudspeth ME, Meganathan R (1996). "Menaquinone (vitamin K2) biosynthesis: localization and characterization of the menE gene from Escherichia coli." Gene 1996;168(1);43-8. PMID: 8626063

Shaw82: Shaw DJ, Guest JR, Meganathan R, Bentley R (1982). "Characterization of Escherichia coli men mutants defective in conversion of o-succinylbenzoate to 1,4-dihydroxy-2-naphthoate." J Bacteriol 152(3);1132-7. PMID: 6754698

Sun12b: Sun Y, Song H, Li J, Jiang M, Li Y, Zhou J, Guo Z (2012). "Active site binding and catalytic role of bicarbonate in 1,4-dihydroxy-2-naphthoyl coenzyme A synthases from vitamin K biosynthetic pathways." Biochemistry 51(22);4580-9. PMID: 22606952

Sun13a: Sun Y, Song H, Li J, Li Y, Jiang M, Zhou J, Guo Z (2013). "Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme A synthase from the crotonase fold superfamily." PLoS One 8(4);e63095. PMID: 23658663

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

UniProt14: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-01 00:00:00." Database.

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

Young75: Young IG (1975). "Biosynthesis of bacterial menaquinones. Menaquinone mutants of Escherichia coli." Biochemistry 14(2);399-406. PMID: 1091286

Other References Related to Gene Regulation

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137


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 19.0 on Wed Sep 2, 2015, biocyc12.