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Literature summary 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 .
    View publication on PubMed

Application

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

Cloned(Commentary)

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

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.5.1.88 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

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

Metals/Ions

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

Organism

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

Substrates and Products (Substrate)

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

Subunits

EC Number Subunits Comment Organism
3.5.1.88 More enzyme structure analysis Xanthomonas oryzae pv. oryzae

Synonyms

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

General Information

EC Number General Information Comment Organism
3.5.1.88 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