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Escherichia coli K-12 substr. MG1655 Enzyme: glutamate racemase



Gene: murI Accession Numbers: EG11204 (EcoCyc), b3967, ECK3959

Synonyms: yijA, dga, glr

Regulation Summary Diagram: ?

Summary:
Glutamate racemase (MurI) catalyzes the racemization of L-glutamate to D-glutamate, an essential component that is unique to bacterial peptidoglycan [Doublet92, Doublet93, Doublet94].

Physiological concentrations of UDP-N-acetylmuramyl-L-Ala, the second substrate of the subsequent reaction in peptidoglycan biosynthesis, specifically activates the enzyme [Doublet94]. It was suggested that the unique N terminus of MurI is required for activation [Ho95]; however, an N-terminally truncated enzyme is still activated by UDP-N-acetylmuramyl-L-Ala [Doublet96]. Site-directed mutagenesis of the two conserved cysteine residues showed that they are essential for enzymatic activity, suggesting that they are involved in the two-base reaction mechanism [Ho95, Doublet96].

Evidence regarding the quarternary structure of MurI was contradictory: [Yoshimura93] reported a homodimer, while [Doublet94] report that the enzyme is monomeric. A crystal structure of MurI in complex with UDP-N-acetylmuramyl-L-Ala has been solved at 1.9 Å resolution and shows a monomer. The activator binds in a hinge region opposite to the catalytically active site [Lundqvist07].

Activated MurI appears to inhibit DNA gyrase activity [Ashiuchi02].

A D-glutamate-requiring strain first isolated in the E. coli B background carries two independent mutations, one in the glutamate transporter GltS and a second in MurI [Dougherty93, Doublet93]. murI is an essential gene [Doublet93, Baliko93].

Peptide inhibitors of glutamate racemase activity have been identified [Kim00c].

Dga: "D-glutamate auxotrophy"

Glr: "glutamate racemase" [Yoshimura93]

Review: [Typas12]

Citations: [Baliko88, Pucci94, Hufton95, Ashiuchi95, Liu98c]

Map Position: [4,163,451 -> 4,164,308] (89.74 centisomes)
Length: 858 bp / 285 aa

Molecular Weight of Polypeptide: 31.002 kD (from nucleotide sequence), 31.0 kD (experimental) [Doublet93 ]

pI: 5.57

Unification Links: ASAP:ABE-0012989 , CGSC:29401 , DIP:DIP-10283N , EchoBASE:EB1189 , EcoGene:EG11204 , EcoliWiki:b3967 , Mint:MINT-1222611 , ModBase:P22634 , OU-Microarray:b3967 , PortEco:murI , PR:PRO_000023319 , Pride:P22634 , Protein Model Portal:P22634 , RefSeq:NP_418402 , RegulonDB:EG11204 , SMR:P22634 , String:511145.b3967 , UniProt:P22634

Relationship Links: InterPro:IN-FAMILY:IPR001920 , InterPro:IN-FAMILY:IPR004391 , InterPro:IN-FAMILY:IPR015942 , InterPro:IN-FAMILY:IPR018187 , Panther:IN-FAMILY:PTHR21198 , PDB:Structure:2JFN , Pfam:IN-FAMILY:PF01177 , Prosite:IN-FAMILY:PS00923 , Prosite:IN-FAMILY:PS00924

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009252 - peptidoglycan biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA06, GOA01a, Doublet93]
GO:0006807 - nitrogen compound metabolic process Inferred by computational analysis [GOA01a]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0008360 - regulation of cell shape Inferred by computational analysis [UniProtGOA11a]
GO:0071555 - cell wall organization Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0008881 - glutamate racemase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Doublet94]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016855 - racemase and epimerase activity, acting on amino acids and derivatives Inferred by computational analysis [GOA01a]
GO:0036361 - racemase activity, acting on amino acids and derivatives Inferred by computational analysis [GOA01a]

MultiFun Terms: cell structure murein
metabolism biosynthesis of macromolecules (cellular constituents) murein (peptidoglycan)

Essentiality data for murI knockouts: ?

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

Credits:
Last-Curated ? 16-Jul-2013 by Keseler I , SRI International


Enzymatic reaction of: glutamate racemase

EC Number: 5.1.1.3

L-glutamate <=> D-glutamate

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. [Doublet94]

Alternative Substrates for L-glutamate: L-homocysteate [Ho95 ]

In Pathways: peptidoglycan biosynthesis I (meso-diaminopimelate containing) , UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (meso-DAP-containing)

Summary:
The equilibrium constant of the reaction is 1.1 [Doublet94].

The kinetic constants reported below were measured in the presence of 6.5 µM UDP-N-acetylmuramyl-L-Ala [Ho95].

Activators (Unknown Mechanism): UDP-N-acetylmuramoyl-L-alanine [Doublet94, Ho95]

Primary Physiological Regulators of Enzyme Activity: UDP-N-acetylmuramoyl-L-alanine

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Vmax (µmol mg-1 min-1)
Citations
D-glutamate
43.33
[Lundqvist07, BRENDA14]
D-glutamate
4200.0
34.0
[Ho95]
L-glutamate
1200.0
0.41, 12.16
[Lundqvist07, BRENDA14]
L-glutamate
2100.0
23.0
[Ho95]

T(opt): 37 °C [Doublet94]

pH(opt): 7.8 [Doublet94]


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b3967 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11204; confirmed by SwissProt match.


References

Ashiuchi02: Ashiuchi M, Kuwana E, Yamamoto T, Komatsu K, Soda K, Misono H (2002). "Glutamate racemase is an endogenous DNA gyrase inhibitor." J Biol Chem 277(42);39070-3. PMID: 12213801

Ashiuchi95: Ashiuchi M, Yoshimura T, Kitamura T, Kawata Y, Nagai J, Gorlatov S, Esaki N, Soda K (1995). "In vivo effect of GroESL on the folding of glutamate racemase of Escherichia coli." J Biochem 117(3);495-8. PMID: 7629013

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

Baliko88: Baliko G, Raukas A, Boros I, Venetianer P (1988). "An Escherichia coli gene in search of a function." Mol Gen Genet 211(2);326-31. PMID: 2832706

Baliko93: Baliko G, Venetianer P (1993). "An Escherichia coli gene in search of a function: phenotypic effects of the gene recently identified as murI." J Bacteriol 175(20);6571-7. PMID: 8407834

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

Doublet92: Doublet P, van Heijenoort J, Mengin-Lecreulx D (1992). "Identification of the Escherichia coli murI gene, which is required for the biosynthesis of D-glutamic acid, a specific component of bacterial peptidoglycan." J Bacteriol 1992;174(18);5772-9. PMID: 1355768

Doublet93: Doublet P, van Heijenoort J, Bohin JP, Mengin-Lecreulx D (1993). "The murI gene of Escherichia coli is an essential gene that encodes a glutamate racemase activity." J Bacteriol 1993;175(10);2970-9. PMID: 8098327

Doublet94: Doublet P, van Heijenoort J, Mengin-Lecreulx D (1994). "The glutamate racemase activity from Escherichia coli is regulated by peptidoglycan precursor UDP-N-acetylmuramoyl-L-alanine." Biochemistry 33(17);5285-90. PMID: 8172902

Doublet96: Doublet P, van Heijenoort J, Mengin-Lecreulx D (1996). "Regulation of the glutamate racemase of Escherichia coli investigated by site-directed mutagenesis." Microb Drug Resist 2(1);43-9. PMID: 9158721

Dougherty93: Dougherty TJ, Thanassi JA, Pucci MJ (1993). "The Escherichia coli mutant requiring D-glutamic acid is the result of mutations in two distinct genetic loci." J Bacteriol 175(1);111-6. PMID: 8093236

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."

Ho95: Ho HT, Falk PJ, Ervin KM, Krishnan BS, Discotto LF, Dougherty TJ, Pucci MJ (1995). "UDP-N-acetylmuramyl-L-alanine functions as an activator in the regulation of the Escherichia coli glutamate racemase activity." Biochemistry 1995;34(8);2464-70. PMID: 7873525

Hufton95: Hufton SE, Ward RJ, Bunce NA, Armstrong JT, Fletcher AJ, Glass RE (1995). "Structure-function analysis of the vitamin B12 receptor of Escherichia coli by means of informational suppression." Mol Microbiol 15(2);381-93. PMID: 7746157

Kim00c: Kim WC, Rhee HI, Park BK, Suk KH, Cha SH (2000). "Isolation of peptide ligands that inhibit glutamate racemase activity from a random phage display library." J Biomol Screen 5(6);435-40. PMID: 11598461

Liu98c: Liu L, Yoshimura T, Endo K, Kishimoto K, Fuchikami Y, Manning JM, Esaki N, Soda K (1998). "Compensation for D-glutamate auxotrophy of Escherichia coli WM335 by D-amino acid aminotransferase gene and regulation of murI expression." Biosci Biotechnol Biochem 62(1);193-5. PMID: 9501533

Lundqvist07: Lundqvist T, Fisher SL, Kern G, Folmer RH, Xue Y, Newton DT, Keating TA, Alm RA, de Jonge BL (2007). "Exploitation of structural and regulatory diversity in glutamate racemases." Nature 447(7146);817-22. PMID: 17568739

Pucci94: Pucci MJ, Novotny J, Discotto LF, Dougherty TJ (1994). "The Escherichia coli Dga (MurI) protein shares biological activity and structural domains with the Pediococcus pentosaceus glutamate racemase." J Bacteriol 176(2);528-30. PMID: 7904596

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Typas12: Typas A, Banzhaf M, Gross CA, Vollmer W (2012). "From the regulation of peptidoglycan synthesis to bacterial growth and morphology." Nat Rev Microbiol 10(2);123-36. PMID: 22203377

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."

Yoshimura93: Yoshimura T, Ashiuchi M, Esaki N, Kobatake C, Choi SY, Soda K (1993). "Expression of glr (murI, dga) gene encoding glutamate racemase in Escherichia coli." J Biol Chem 268(32);24242-6. PMID: 7901215

Other References Related to Gene Regulation

Aufrere86: Aufrere R, Tempete M, Bohin JP (1986). "Regulation of expression of the gene for vitamin B12 receptor cloned on a multicopy plasmid in Escherichia coli." Mol Gen Genet 1986;205(2);358-65. PMID: 3027510

Gallo08: Gallo S, Oberhuber M, Sigel RK, Krautler B (2008). "The Corrin Moiety of Coenzyme B(12) is the Determinant for Switching the btuB Riboswitch of E. coli." Chembiochem 9(9):1408-14. PMID: 18506875

Lei11: Lei GS, Syu WJ, Liang PH, Chak KF, Hu WS, Hu ST (2011). "Repression of btuB gene transcription in Escherichia coli by the GadX protein." BMC Microbiol 11(1);33. PMID: 21314918

Nou00: Nou X, Kadner RJ (2000). "Adenosylcobalamin inhibits ribosome binding to btuB RNA." Proc Natl Acad Sci U S A 97(13);7190-5. PMID: 10852957


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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 Thu Dec 18, 2014, BIOCYC13A.