Structure of the Oxygen, Pyridoxal Phosphate-Dependent Capuramycin Biosynthetic Protein Cap15

Phillip G. Daniel-Ivad, Steven Van Lanen, Katherine S. Ryan

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Pyridoxal phosphate-dependent enzymes able to use oxygen as a co-substrate have emerged in multiple protein families. Here, we use crystallography to solve the 2.40 Å resolution crystal structure of Cap15, a nucleoside biosynthetic enzyme that catalyzes the oxidative decarboxylation of glycyl uridine. Our structural study captures the internal aldimine, pinpointing the active site lysine as K230 and showing the site of phosphate binding. Our docking studies reveal how Cap15 is able to catalyze a stereoselective deprotonation reaction, and bioinformatic analysis reveals active site residues that distinguish Cap15 from the structurally related d-glucosaminate-6-phosphate ammonia lyase and l-seryl-tRNA(Sec) selenium transferase (SelA). Our work provides the structural basis for further mechanistic investigation of a unique biosynthetic enzyme and provides a blueprint for understanding how oxygen reactivity emerged in the SelA-like protein family.

Original languageEnglish
Pages (from-to)2611-2621
Number of pages11
JournalBiochemistry
Volume62
Issue number17
DOIs
StatePublished - Sep 5 2023

Bibliographical note

Publisher Copyright:
© 2023 American Chemical Society.

ASJC Scopus subject areas

  • Biochemistry

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