Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: o-succinylbenzoate synthase



Gene: menC Accession Numbers: EG11532 (EcoCyc), b2261, ECK2255

Regulation Summary Diagram: ?

Summary:
O-succinylbenzoate synthase catalyzes the formation of the first aromatic intermediate of the menaquinone biosynthetic pathway by dehydration of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate [Sharma93, Palmer99]. MenC belongs to the MLE subfamily of the enolase family of enzymes [Palmer99].

Crystal structures of the ligand-free, mutant enzyme-substrate, and enzyme-product complexes have been solved, and a reaction mechanism has been proposed [Thompson00, Klenchin03]. Site-directed mutagenesis of two proposed active-site lysines, Lys133 and Lys235, yielded catalytically inactive enzymes [Klenchin03].

Review: [Gerlt05]

Gene Citations: [Sharma92, Sharma96]

Locations: cytosol

Map Position: [2,373,022 <- 2,373,984] (51.15 centisomes)
Length: 963 bp / 320 aa

Molecular Weight of Polypeptide: 35.477 kD (from nucleotide sequence)

pI: 5.0

Unification Links: ASAP:ABE-0007473 , CGSC:518 , DIP:DIP-10184N , EchoBASE:EB1494 , EcoGene:EG11532 , EcoliWiki:b2261 , Mint:MINT-1305669 , ModBase:P29208 , OU-Microarray:b2261 , PortEco:menC , PR:PRO_000023202 , Protein Model Portal:P29208 , RefSeq:NP_416764 , RegulonDB:EG11532 , SMR:P29208 , String:511145.b2261 , UniProt:P29208

Relationship Links: InterPro:IN-FAMILY:IPR010196 , InterPro:IN-FAMILY:IPR013342 , PDB:Structure:1FHU , PDB:Structure:1FHV , PDB:Structure:1R6W , PDB:Structure:2OFJ , Pfam:IN-FAMILY:PF01188 , Smart:IN-FAMILY:SM00922

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0009234 - menaquinone biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA06, GOA01, Guest79]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0016836 - hydro-lyase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Palmer99]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA01]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

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

Essentiality data for menC 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:
Last-Curated ? 05-Apr-2007 by Keseler I , SRI International


Enzymatic reaction of: o-succinylbenzoate synthase

Synonyms: OSB synthase, 4-(2'-carboxyphenyl)-4-oxybutyric acid synthase

EC Number: 4.2.1.113

(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate <=> 2-succinylbenzoate + H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

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

Cofactors or Prosthetic Groups: Mg2+ [Thompson00]

Kinetic Parameters:

Substrate
Km (μM)
Citations
(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate
16.0
[Taylor01]

T(opt): 50 °C [BRENDA14, Weische87]

pH(opt): 8.2 [BRENDA14, Weische87]


Sequence Features

Feature Class Location Common Name Citations Comment
Active-Site 133 catalytic base for initial proton abstraction
[Klenchin03]
 
Metal-Binding-Site 161  
[UniProt10]
UniProt: Magnesium;
Sequence-Conflict 176 -> 177  
[Sharma93, UniProt10]
Alternate sequence: KY → missing; UniProt: (in Ref. 1; AAA71917);
Metal-Binding-Site 190  
[UniProt10]
UniProt: Magnesium;
Metal-Binding-Site 213  
[UniProt10]
UniProt: Magnesium;
Active-Site 235  
[UniProt10]
UniProt: Proton acceptor;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b2261 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11532; 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.

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

Gerlt05: Gerlt JA, Babbitt PC, Rayment I (2005). "Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity." Arch Biochem Biophys 433(1);59-70. PMID: 15581566

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."

Guest79: Guest JR (1979). "Anaerobic growth of Escherichia coli K12 with fumarate as terminal electron acceptor. Genetic studies with menaquinone and fluoroacetate-resistant mutants." J Gen Microbiol 115(2);259-71. PMID: 393800

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

Klenchin03: Klenchin VA, Taylor Ringia EA, Gerlt JA, Rayment I (2003). "Evolution of enzymatic activity in the enolase superfamily: structural and mutagenic studies of the mechanism of the reaction catalyzed by o-succinylbenzoate synthase from Escherichia coli." Biochemistry 42(49);14427-33. PMID: 14661953

Meganathan83: Meganathan R, Bentley R (1983). "Thiamine pyrophosphate requirement for o-succinylbenzoic acid synthesis in Escherichia coli and evidence for an intermediate." J Bacteriol 153(2);739-46. PMID: 6337125

Palmer99: Palmer DR, Garrett JB, Sharma V, Meganathan R, Babbitt PC, Gerlt JA (1999). "Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase." Biochemistry 38(14);4252-8. PMID: 10194342

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

Sharma93: Sharma V, Meganathan R, Hudspeth ME (1993). "Menaquinone (vitamin K2) biosynthesis: cloning, nucleotide sequence, and expression of the menC gene from Escherichia coli." J Bacteriol 1993;175(15);4917-21. PMID: 8335646

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

Taylor01: Taylor EA, Palmer DR, Gerlt JA (2001). "The lesser "burden borne" by o-succinylbenzoate synthase: an "easy" reaction involving a carboxylate carbon acid." J Am Chem Soc 123(24);5824-5. PMID: 11403626

Thompson00: Thompson TB, Garrett JB, Taylor EA, Meganathan R, Gerlt JA, Rayment I (2000). "Evolution of enzymatic activity in the enolase superfamily: structure of o-succinylbenzoate synthase from Escherichia coli in complex with Mg2+ and o-succinylbenzoate." Biochemistry 39(35);10662-76. PMID: 10978150

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

Weische87: Weische A, Garvert W, Leistner E (1987). "Biosynthesis of o-succinylbenzoic acid. II: Properties of o-succinylbenzoic acid synthase, an enzyme involved in vitamin K2 biosynthesis." Arch Biochem Biophys 256(1);223-31. PMID: 3300553

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 18.5 on Mon Nov 24, 2014, BIOCYC14B.