Literature summary for 5.1.1.3 extracted from

Lundqvist, T.; Fisher, S.L.; Kern, G.; Folmer, R.H.; Xue, Y.; Newton, D.T.; Keating, T.A.; Alm, R.A.; de Jonge, B.L.
Exploitation of structural and regulatory diversity in glutamate racemases (2007), Nature, 447, 817-822.

Search for more literature for 5.1.1.3

Activating Compound

Activating Compound	Comment	Organism	Structure
additional information	in contrast to Escherichia coli no activation by UDP-MurNAc-Ala, the product of the preceding enzyme in the peptidoglycan biosynthetic pathway	Staphylococcus aureus
additional information	in contrast to Escherichia coli no activation by UDP-MurNAc-Ala, the product of the preceding enzyme in the peptidoglycan biosynthetic pathway	Enterococcus faecalis
additional information	in contrast to Escherichia coli no activation by UDP-MurNAc-Ala, the product of the preceding enzyme in the peptidoglycan biosynthetic pathway	Enterococcus faecium
additional information	in contrast to Escherichia coli no activation by UDP-MurNAc-Ala, the product of the preceding enzyme in the peptidoglycan biosynthetic pathway	Helicobacter pylori
UDP-MurNAc-Ala	strong activation by UDP-MurNAc-Ala, the product of the preceding enzyme in the peptidoglycan biosynthetic pathway	Escherichia coli

Application

Application	Comment	Organism
drug development	glutamate racemase is an enzyme essential to the bacterial cell wall biosynthesis pathway, and is therefore considered as a target for antibacterial drug discovery	Staphylococcus aureus
drug development	glutamate racemase is an enzyme essential to the bacterial cell wall biosynthesis pathway, and is therefore considered as a target for antibacterial drug discovery	Escherichia coli
drug development	glutamate racemase is an enzyme essential to the bacterial cell wall biosynthesis pathway, and is therefore considered as a target for antibacterial drug discovery	Enterococcus faecalis
drug development	glutamate racemase is an enzyme essential to the bacterial cell wall biosynthesis pathway, and is therefore considered as a target for antibacterial drug discovery	Enterococcus faecium
drug development	glutamate racemase is an enzyme essential to the bacterial cell wall biosynthesis pathway, and is therefore considered as a target for antibacterial drug discovery	Helicobacter pylori

Cloned(Commentary)

Cloned (Comment)	Organism
full-length MurI proteins are prepared by expression either as native (Helicobacter pylori, Escherichia coli) or N-terminal 6xHis-tagged (Staphylococcus aureus, Enterococcus faecalis, Enterococcus faecium) recombinant proteins in Escherichia coli strains co-expressing the chaperone proteins GroEL/GroES27 and purified by standard chromatographic methods	Staphylococcus aureus
full-length MurI proteins are prepared by expression either as native (Helicobacter pylori, Escherichia coli) or N-terminal 6xHis-tagged (Staphylococcus aureus, Enterococcus faecalis, Enterococcus faecium) recombinant proteins in Escherichia coli strains co-expressing the chaperone proteins GroEL/GroES27 and purified by standard chromatographic methods	Escherichia coli
full-length MurI proteins are prepared by expression either as native (Helicobacter pylori, Escherichia coli) or N-terminal 6xHis-tagged (Staphylococcus aureus, Enterococcus faecalis, Enterococcus faecium) recombinant proteins in Escherichia coli strains co-expressing the chaperone proteins GroEL/GroES27 and purified by standard chromatographic methods	Enterococcus faecalis
full-length MurI proteins are prepared by expression either as native (Helicobacter pylori, Escherichia coli) or N-terminal 6xHis-tagged (Staphylococcus aureus, Enterococcus faecalis, Enterococcus faecium) recombinant proteins in Escherichia coli strains co-expressing the chaperone proteins GroEL/GroES27 and purified by standard chromatographic methods	Enterococcus faecium
full-length MurI proteins are prepared by expression either as native (Helicobacter pylori, Escherichia coli) or N-terminal 6xHis-tagged (Staphylococcus aureus, Enterococcus faecalis, Enterococcus faecium) recombinant proteins in Escherichia coli strains co-expressing the chaperone proteins GroEL/GroES27 and purified by standard chromatographic methods	Helicobacter pylori

Crystallization (Commentary)

Crystallization (Comment)	Organism
crystal structures of MurI of Helicobacter pylori, Escherichia coli, Staphylococcus aureus, Enterococcus faecalis and Enterococcus faecium are analysed under similar, physiologically relevant conditons. MurI of Staphylococcus aureus, Enterococcus faecalis and Enterococcus faecium all form homodimeric structures. In all these structures, monomers oligomerize in a tail-to-tail orientation with active sites opposed and fully exposed to solvent	Staphylococcus aureus
crystal structures of MurI of Helicobacter pylori, Escherichia coli, Staphylococcus aureus, Enterococcus faecalis and Enterococcus faecium are analysed under similar, physiologically relevant conditons. MurI of Staphylococcus aureus, Enterococcus faecalis and Enterococcus faecium all form homodimeric structures. In all these structures, monomers oligomerize in a tail-to-tail orientation with active sites opposed and fully exposed to solvent	Enterococcus faecalis
crystal structures of MurI of Helicobacter pylori, Escherichia coli, Staphylococcus aureus, Enterococcus faecalis and Enterococcus faecium are analysed under similar, physiologically relevant conditons. MurI of Staphylococcus aureus, Enterococcus faecalis and Enterococcus faecium all form homodimeric structures. In all these structures, monomers oligomerize in a tail-to-tail orientation with active sites opposed and fully exposed to solvent	Enterococcus faecium
crystal structures of MurI of Helicobacter pylori, Escherichia coli, Staphylococcus aureus, Enterococcus faecalis and Enterococcus faecium are analysed under similar, physiologically relevant conditons. The Escherichia coli MurI co-crystallizes as a monomer with both L-glutamate and its activator UDP-MurNAc-Ala. The activator binds in the hinge region on the side opposite to the catalytically active site through contacts between the uracil ring system and domain B and through specific salt bridge interactions with R104 in domain A and the alanyl moiety of the activator, consistent with the strict requirement of the alanine and uracil moieties for activation	Escherichia coli
the different kinetic profiles of MurI enzymes across the species suggest fundamental structural differences and therefore, crystal structures of MurI of Helicobacter pylori, Escherichia coli, Staphylococcus aureus, Enterococcus faecalis and Enterococcus faecium are analysed under similar, physiologically relevant conditons. The Helicobacter pylori MurI enzyme also forms a homodimer but with the active sites in close proximity in a face-to-face orientation	Helicobacter pylori

Protein Variants

Protein Variants	Comment	Organism
A75T	Ki: 0.661 mM (inhibitor: D-glutamate). Turnover number: 1.78/sec (substrate: L-glutamate), 0.065/sec (substrate: D-glutamate). Km: 7.4 mM (substrate: L-glutamate), Km: 0.275 mM (substrate: D-glutamate)	Helicobacter pylori
E151T	Ki: 100 mM (value above 100 for inhibitor: D-glutamate). Turnover number: 0.08/sec (substrate: D-glutamate), 2.26/sec (substrate: L-glutamate). Km: 7.36 mM (substrate: L-glutamate), Km: 0.282 mM (substrate: D-glutamate)	Helicobacter pylori

Inhibitors

Inhibitors	Comment	Organism	Structure
5-methyl-7-(2-methylpropyl)-2-(naphthalen-1-ylmethyl)-3-pyridin-4-yl-2H-pyrazolo[3,4-d]pyrimidine-4,6(5H,7H)-dione	a pyrazolopyrimidinedione analogue identified by a high-throughput screen demonstrates inhibition with excellent selectivity for MurI of Helicobacter pylori, it is time-independent, fully-reversible and insensitive to changes in enzyme or detergent concentration	Helicobacter pylori
D-glutamate	MurI of Helicobacter pylori is strongly inhibited by D-glutamate	Helicobacter pylori
additional information	in contrast to MurI of Helicobacter pylori no inhibition by D-glutamate	Enterococcus faecalis
additional information	in contrast to MurI of Helicobacter pylori no inhibition by D-glutamate	Enterococcus faecium
additional information	in contrast to MurI of Helicobacter pylori no inhibition by D-glutamate	Escherichia coli
additional information	in contrast to MurI of Helicobacter pylori no inhibition by D-glutamate	Staphylococcus aureus

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
0.014	-	D-glutamate	-	Staphylococcus aureus
0.063	-	D-glutamate	-	Helicobacter pylori
0.24	-	D-glutamate	-	Enterococcus faecium
0.25	-	D-glutamate	-	Enterococcus faecalis
0.275	-	D-glutamate	deletion mutant A75T	Helicobacter pylori
0.282	-	D-glutamate	deletion mutant E151T	Helicobacter pylori
0.74	-	L-glutamate	demonstrates a high degree of asymmetry in substrate processing with the Michaelis constant for D-glutamate approximately tenfold lower than for L-glutamate	Helicobacter pylori
1.1	-	L-glutamate	-	Enterococcus faecium
1.2	-	L-glutamate	-	Escherichia coli
1.2	-	L-glutamate	-	Enterococcus faecalis
2.1	-	D-glutamate	-	Escherichia coli
4.6	-	L-glutamate	-	Staphylococcus aureus
7.36	-	L-glutamate	deletion mutant E151T	Helicobacter pylori
7.4	-	L-glutamate	deletion mutant A75T	Helicobacter pylori

Organism

Organism	UniProt	Comment	Textmining
Enterococcus faecalis	-	-	-
Enterococcus faecium	-	-	-
Escherichia coli	-	-	-
Helicobacter pylori	-	-	-
Staphylococcus aureus	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
enzyme is purified by using standard chromatographic methods	Staphylococcus aureus
enzyme is purified by using standard chromatographic methods	Escherichia coli
enzyme is purified by using standard chromatographic methods	Enterococcus faecalis
enzyme is purified by using standard chromatographic methods	Enterococcus faecium
enzyme is purified by using standard chromatographic methods	Helicobacter pylori

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg]	Specific Activity Maximum [µmol/min/mg]	Comment	Organism
additional information	-	Escherichia coli MurI is monomeric in solution and shows extremely low intrinsic activity in either direction (symmetrical kinetic profile), but catalytic turnover is upregulated over 1000fold by UDP-MurNAc-Ala, the product of the preceding enzyme in the peptidoglycan biosynthetic pathway	Escherichia coli

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
L-glutamate	-	Escherichia coli	D-glutamate	-	r
L-glutamate	-	Helicobacter pylori	D-glutamate	-	r
L-glutamate	MurI enzymes from the Gram-positive species Staphylococcus aureus, Enterococcus faecalis and Enterococcus faecium share similar biophysical and biochemical characteristics that are distinct from Escherichia coli and Helicobacter pylori MurI	Staphylococcus aureus	D-glutamate	-	r
L-glutamate	MurI enzymes from the Gram-positive species Staphylococcus aureus, Enterococcus faecalis and Enterococcus faecium share similar biophysical and biochemical characteristics that are distinct from Escherichia coli and Helicobacter pylori MurI	Enterococcus faecalis	D-glutamate	-	r
L-glutamate	MurI enzymes from the Gram-positive species Staphylococcus aureus, Enterococcus faecalis and Enterococcus faecium share similar biophysical and biochemical characteristics that are distinct from Escherichia coli and Helicobacter pylori MurI	Enterococcus faecium	D-glutamate	-	r

Subunits

Subunits	Comment	Organism
homodimer	method: gel filtration. The Helicobacter pylori MurI enzyme also forms a homodimer but with the active sites in close proximity in a face-to-face orientation	Helicobacter pylori
monomer	gel filtration	Staphylococcus aureus
monomer	gel filtration	Escherichia coli
monomer	gel filtration	Enterococcus faecalis
monomer	gel filtration	Enterococcus faecium

Synonyms

Synonyms	Comment	Organism
glutamate racemase	-	Staphylococcus aureus
glutamate racemase	-	Escherichia coli
glutamate racemase	-	Enterococcus faecalis
glutamate racemase	-	Enterococcus faecium
glutamate racemase	-	Helicobacter pylori
MurI	-	Staphylococcus aureus
MurI	-	Escherichia coli
MurI	-	Enterococcus faecalis
MurI	-	Enterococcus faecium
MurI	-	Helicobacter pylori

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
0.065	-	D-glutamate	deletion mutant A75T	Helicobacter pylori
0.08	-	D-glutamate	deletion mutant E151T	Helicobacter pylori
0.2	-	D-glutamate	-	Helicobacter pylori
0.41	-	L-glutamate	-	Escherichia coli
0.41	-	D-glutamate	-	Enterococcus faecalis
0.56	-	D-glutamate	-	Staphylococcus aureus
1.05	-	L-glutamate	-	Helicobacter pylori
1.78	-	L-glutamate	deletion mutant A75T	Helicobacter pylori
2.26	-	L-glutamate	deletion mutant E151T	Helicobacter pylori
3.4	-	L-glutamate	-	Enterococcus faecium
8.5	-	L-glutamate	-	Staphylococcus aureus
11.73	-	D-glutamate	-	Enterococcus faecalis
12.16	-	L-glutamate	-	Escherichia coli
15	-	D-glutamate	-	Enterococcus faecium
25	-	L-glutamate	-	Enterococcus faecalis
36.66	-	L-glutamate	-	Enterococcus faecium
43.33	-	D-glutamate	-	Escherichia coli

Ki Value [mM]

Ki Value [mM]	Ki Value maximum [mM]	Inhibitor	Comment	Organism	Structure
0.0058	-	D-glutamate	-	Helicobacter pylori
0.661	-	D-glutamate	deletion mutant A75T	Helicobacter pylori
100	-	D-glutamate	value above 100 for deletion mutant E151K	Helicobacter pylori

IC50 Value

IC50 Value	IC50 Value Maximum	Comment	Organism	Inhibitor	Structure
0.0014	-	a pyrazolopyrimidinedione analogue (compound A) identified by a high-throughput screen demonstrates inhibition with excellent selectivity for MurI of Helicobacter pylori, it is time-independent, fully-reversible and insensitive to changes in enzyme or detergent concentration	Helicobacter pylori	pyrazolopyrimidinedione analogue
0.4	-	value above 0.4, a pyrazolopyrimidinedione analogue (compound A) identified by a high-throughput screen demonstrates inhibition with excellent selectivity for MurI of Helicobacter pylori but not for MurI of Escherichia coli	Escherichia coli	pyrazolopyrimidinedione analogue
0.4	-	value above 0.4, a pyrazolopyrimidinedione analogue (compound A) identified by a high-throughput screen demonstrates inhibition with excellent selectivity for MurI of Helicobacter pylori but not for MurI of Staphylococcus aureus	Staphylococcus aureus	pyrazolopyrimidinedione analogue

Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.

Release 2023.1 (January 2023)