Literature summary for 3.5.1.88 extracted from

Ngo, H.P.; Ho, T.H.; Lee, I.; Tran, H.T.; Sur, B.; Kim, S.; Kim, J.G.; Ahn, Y.J.; Cha, S.S.; Kang, L.W.
Crystal structures of peptide deformylase from rice pathogen Xanthomonas oryzae pv. oryzae in complex with substrate peptides, actinonin, and fragment chemical compounds (2016), J. Agric. Food Chem., 64, 7307-7314 .

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Application

Application	Comment	Organism
drug development	the enzyme is an important target to develop antibacterial agents	Xanthomonas oryzae pv. oryzae

Cloned(Commentary)

Cloned (Comment)	Organism
gene def, sequence comparisons, recombinant expression	Xanthomonas oryzae pv. oryzae

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified enzyme in complex with product peptides Met-Ala-Ser and Met-Ala, with inhibitor actinonin, and with six fragment chemical compounds bound in the substrate-binding pocket, X-ray diffraction structure determination and analysis at 1.9 A resolution	Xanthomonas oryzae pv. oryzae

Inhibitors

Inhibitors	Comment	Organism	Structure
actinonin	analysis of the binding structure to XoPDF	Xanthomonas oryzae pv. oryzae
additional information	actinonin binding structure comparisons of enzymes from different sources	Xanthomonas oryzae pv. oryzae

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Cd2+	the metal ion is bound in the active site, metalloprotease, metal binding and coordination structure of enzyme XoPDF	Xanthomonas oryzae pv. oryzae
additional information	comparisons to Escherichia coli metal binding structures with Co2+ and Fe2+	Xanthomonas oryzae pv. oryzae
Zn2+	the metal ion is bound in the active site, metalloprotease, metal binding and coordination structure of enzyme XoPDF	Xanthomonas oryzae pv. oryzae

Organism

Organism	UniProt	Comment	Textmining
Xanthomonas oryzae pv. oryzae	Q5H3Z2	-	-
Xanthomonas oryzae pv. oryzae KACC10331	Q5H3Z2	-	-
Xanthomonas oryzae pv. oryzae KXO85	Q5H3Z2	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
formyl-Met-Ala + H2O	-	Xanthomonas oryzae pv. oryzae	formate + Met-Ala	-	?
formyl-Met-Ala + H2O	-	Xanthomonas oryzae pv. oryzae KACC10331	formate + Met-Ala	-	?
formyl-Met-Ala + H2O	-	Xanthomonas oryzae pv. oryzae KXO85	formate + Met-Ala	-	?
formyl-Met-Ala-Ser + H2O	-	Xanthomonas oryzae pv. oryzae	formate + Met-Ala-Ser	-	?
formyl-Met-Ala-Ser + H2O	-	Xanthomonas oryzae pv. oryzae KACC10331	formate + Met-Ala-Ser	-	?
formyl-Met-Ala-Ser + H2O	-	Xanthomonas oryzae pv. oryzae KXO85	formate + Met-Ala-Ser	-	?

Subunits

Subunits	Comment	Organism
More	enzyme structure analysis	Xanthomonas oryzae pv. oryzae

Synonyms

Synonyms	Comment	Organism
DEF	-	Xanthomonas oryzae pv. oryzae
PDF	-	Xanthomonas oryzae pv. oryzae
XOO1075	-	Xanthomonas oryzae pv. oryzae
XoPDF	-	Xanthomonas oryzae pv. oryzae

General Information

General Information	Comment	Organism
physiological function	peptide deformylase (PDF) catalyzes the removal of the N-formyl group from the N-terminus of newly synthesized polypeptides in bacterial cells	Xanthomonas oryzae pv. oryzae

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Release 2023.1 (January 2023)