Literature summary for 6.3.2.10 extracted from

Cha, S.S.; An, Y.J.; Jeong, C.S.; Yu, J.H.; Chung, K.M.
ATP-binding mode including a carbamoylated lysine and two Mg(2+) ions, and substrate-binding mode in Acinetobacter baumannii MurF (2014), Biochem. Biophys. Res. Commun., 450, 1045-1050 .

Application

Application	Comment	Organism
drug development	AbMurF is a target for the structure-based development of inhibitors to treat Acinetobacter baumannii infections	Acinetobacter baumannii

Cloned(Commentary)

Cloned (Comment)	Organism
gene murF, recombinant expression of His-tagged selenomethionine-substituted enzyme in Escherichia coli strain B834(DE3)	Acinetobacter baumannii

Crystallization (Commentary)

Crystallization (Comment)	Organism
crystallization of two MurF-ATP complexes: the MurFATP complex and the MurF-ATP-UDP complex, trigonal crystals of Se-AbMurF with ATP are grown in a precipitant solution containing 20% w/v PEG 3000 and 0.1 M sodium citrate-citric acid, pH 5.5, crystals of the AbMurF-ATP-UDP complex are obtained by soaking experiments, trigonal crystals of the AbMurF-ATP complex isomorphous to those of the Se-AbMurF-ATP complex are grown in the mother liquor and are then transferred to a solution containing 20% glycerol, 20% PEG 3000, 0.1 M sodium citrate-citric acid, pH 5.5, and 15 mM UDP, 25 min soaking, monoclinic crystals of the AbMurF-ATP complex are grown in a precipitant solution containing 24% PEG 4000, 0.08 M Tris-HCl, pH 8.5, 0.16 M MgCl2, and 20% glycerol by the micro-batch crystallization method at 22°C, X-ray diffraction structure determination and analysis at 1.8-2.8 A resolution	Acinetobacter baumannii

Crystallization (Comment)

Organism

crystallization of two MurF-ATP complexes: the MurFATP complex and the MurF-ATP-UDP complex, trigonal crystals of Se-AbMurF with ATP are grown in a precipitant solution containing 20% w/v PEG 3000 and 0.1 M sodium citrate-citric acid, pH 5.5, crystals of the AbMurF-ATP-UDP complex are obtained by soaking experiments, trigonal crystals of the AbMurF-ATP complex isomorphous to those of the Se-AbMurF-ATP complex are grown in the mother liquor and are then transferred to a solution containing 20% glycerol, 20% PEG 3000, 0.1 M sodium citrate-citric acid, pH 5.5, and 15 mM UDP, 25 min soaking, monoclinic crystals of the AbMurF-ATP complex are grown in a precipitant solution containing 24% PEG 4000, 0.08 M Tris-HCl, pH 8.5, 0.16 M MgCl2, and 20% glycerol by the micro-batch crystallization method at 22°C, X-ray diffraction structure determination and analysis at 1.8-2.8 A resolution

Acinetobacter baumannii

Localization

Localization	Comment	Organism	GeneOntology No.	Textmining
cytosol	-	Acinetobacter baumannii	5829	-

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required, the ATP-binding mode revealed by the crystal structure of the MurF-ATP complex confirms that a carbamoylated lysine and two Mg2+ ions are required for enzyme activity of MurF	Acinetobacter baumannii

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
ATP + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysine + D-alanyl-D-alanine	Acinetobacter baumannii	-	ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine	-	?
ATP + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysine + D-alanyl-D-alanine	Acinetobacter baumannii AB307-0294	-	ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine	-	?

Organism

Organism	UniProt	Comment	Textmining
Acinetobacter baumannii	A0A0J9X1Z8	-	-
Acinetobacter baumannii AB307-0294	A0A0J9X1Z8	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged enzyme from Escherichia coli strain B834(DE3) by nickel affinity chromatography, gel filtration, and ultrafiltration	Acinetobacter baumannii

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
ATP + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysine + D-alanyl-D-alanine	-	Acinetobacter baumannii	ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine	-	?
ATP + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysine + D-alanyl-D-alanine	ATP and UDP binding mode analysis, overview	Acinetobacter baumannii	ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine	-	?
ATP + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysine + D-alanyl-D-alanine	-	Acinetobacter baumannii AB307-0294	ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine	-	?
ATP + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysine + D-alanyl-D-alanine	ATP and UDP binding mode analysis, overview	Acinetobacter baumannii AB307-0294	ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine	-	?
additional information	the ATP-binding mode revealed by the crystal structure of the MurF-ATP complex confirms that a carbamoylated lysine and two Mg2+ ions are required for enzyme activity of MurF. UDP-MurF interactions are observed in the crystal structure of the MurF-ATP-UDP complex, depicting the characteristic substrate-binding mode of MurF. Structure-function analysis, overview	Acinetobacter baumannii	?	-	?
additional information	the ATP-binding mode revealed by the crystal structure of the MurF-ATP complex confirms that a carbamoylated lysine and two Mg2+ ions are required for enzyme activity of MurF. UDP-MurF interactions are observed in the crystal structure of the MurF-ATP-UDP complex, depicting the characteristic substrate-binding mode of MurF. Structure-function analysis, overview	Acinetobacter baumannii AB307-0294	?	-	?

Synonyms

Synonyms	Comment	Organism
AbMurF	-	Acinetobacter baumannii
MurF	-	Acinetobacter baumannii

Cofactor

Cofactor	Comment	Organism	Structure
ATP	the ATP-binding mode revealed by the crystal structure of the MurF-ATP complex confirms that a carbamoylated lysine and two Mg2+ ions are required for enzyme activity of MurF	Acinetobacter baumannii

General Information

General Information	Comment	Organism
physiological function	MurF adds D-Ala-D-Ala dipeptide to UDP-N-acetylmuramyl-L-Ala-c-D-Glu-m-DAP (or L-Lys) in an ATP-dependent manner, which is the last step in the biosynthesis of monomeric precursor of peptidoglycan for bacterial cell wall synthesis	Acinetobacter baumannii