Literature summary for 6.3.2.4 extracted from

Neuhaus, F.C.
Role of Arg301 in substrate orientation and catalysis in subsite 2 of D-alanine:D-alanine (D-lactate) ligase from Leuconostoc mesenteroides: A molecular docking study (2010), J. Mol. Graph. Model., 28, 728-734.

Crystallization (Commentary)

Crystallization (Comment)	Organism
molecular docking study on the orientations of substrates. Residue Arg301 has a dual function in a sequential reaction mechanism, i.e. substrate orientation in subsite 2 as well as stabilization of the transition state. With D-lactate a bifurcated H-bond from Arg301 to the R-OH of D-lactate may account for its orientation and nucleophile activation. This orientation is observed when the guanidino side chain of this residue is flexible. D-Ala adopts an orientation that utilizes H-bonding to water 2882 and the D-Ala phosphate in subsite 1. Both of these orientations provide mechanisms of deprotonation and place the nucleophile within 3.2 A of the electrophilic carbonyl of the D-Ala phosphate intermediate for formation of the transition state	Leuconostoc mesenteroides

Crystallization (Comment)

Organism

molecular docking study on the orientations of substrates. Residue Arg301 has a dual function in a sequential reaction mechanism, i.e. substrate orientation in subsite 2 as well as stabilization of the transition state. With D-lactate a bifurcated H-bond from Arg301 to the R-OH of D-lactate may account for its orientation and nucleophile activation. This orientation is observed when the guanidino side chain of this residue is flexible. D-Ala adopts an orientation that utilizes H-bonding to water 2882 and the D-Ala phosphate in subsite 1. Both of these orientations provide mechanisms of deprotonation and place the nucleophile within 3.2 A of the electrophilic carbonyl of the D-Ala phosphate intermediate for formation of the transition state

Leuconostoc mesenteroides

Organism

Organism	UniProt	Comment	Textmining
Leuconostoc mesenteroides	-	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
ATP + 2 D-Ala	-	Leuconostoc mesenteroides	ADP + phosphate + D-Ala-D-Ala	-	?
ATP + D-Ala + D-lactate	-	Leuconostoc mesenteroides	ADP + phosphate + D-Ala-D-lactate	depsipeptide D-Ala-D-lactate is responsible for the intrinsic resistance of Leuconostoc mesenteroides to vancomycin	?

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Release 2023.1 (January 2023)