Comparative folding analyses of unknotted versus trefoil-knotted ornithine transcarbamylases suggest stabilizing effects of protein knots

Journal Article · Sat Sep 15 04:00:00 EDT 2018 · Biochemical and Biophysical Research Communications

DOI:https://doi.org/10.1016/J.BBRC.2018.06.082· OSTI ID:23105676

Sriramoju, Manoj Kumar ^[1]; Yang, Tzu-Jing

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1. Institute of Biological Chemistry, Academia Sinica, Taipei, 11529 (China)

Highlights: • The OTC superfamily contains both knotted and unknotted members that can be used to explore the advantages of being knotted. • SAXS confirms that homotrimeric quaternary structures of the unknotted EcOTC and trefoil knotted BfSOTC and XcAOTC. • Knotted BfSOTC and XcAOTC are more resistant to chemical denaturation than does the unknotted EcOTC. • HDX-MS revealed attenuated local fluctuations within the knotted BfSOTC and XcAOTC whereas the unknotted EcOTC exhibited more abundant local unfolding events. • Our results suggest a stabilizing role of folding dynamics for protein knots. Ornithine transcarbamylases (OTCs) are conserved enzymes involved in arginine biosynthesis in microbes and the urea cycle in mammals. Recent bioinformatics analyses identified two unique OTC variants, N-succinyl-l-ornithine transcarbamylase from Bacteroides fragilis (BfSOTC) and N-acetyl-l-ornithine transcarbamylase from Xanthomonas campestris (XcAOTC). These two variants diverged from other OTCs during evolution despite sharing the common tertiary and quaternary structures, with the exception that the substrate recognition motifs are topologically knotted. The OTC family therefore offers a unique opportunity for investigating the importance of protein knots in biological functions and folding stabilities. Using hydrogen-deuterium exchange-coupled mass spectrometry, we compared the native dynamics of BfSOTC and XcAOTC with respect to the unknotted ornithine transcarbamylase from Escherichia coli (EcOTC). Our results suggest that, in addition to substrate specificity, the knotted structures in XcAOTC and BfSOTC may play an important role in stabilizing the folding dynamics, particularly around the knotted structural elements.

• OSTI ID: 23105676
• Journal Information: Biochemical and Biophysical Research Communications, Journal Name: Biochemical and Biophysical Research Communications Journal Issue: 2 Vol. 503; ISSN 0006-291X; ISSN BBRCA9
• Country of Publication: United States
• Language: English

Related Subjects

60 APPLIED LIFE SCIENCES
ARGININE
ENZYMES
ESCHERICHIA COLI
ORNITHINE