Structural mechanism of Escherichia coli cyanase

Kim, Jihan; Kim, Youngchang; Park, Jaehyun; Nam, Ki Hyun; Cho, Yunje

doi:10.1107/s2059798323009609

Structural mechanism of Escherichia coli cyanase

Journal Article · Fri Dec 01 00:00:00 EST 2023 · Acta Crystallographica. Section D. Structural Biology

DOI:https://doi.org/10.1107/s2059798323009609· OSTI ID:2566861

Kim, Jihan ^[1]; ^[2]; ^[1]; ^[3]; Cho, Yunje ^[1]

Pohang Univ. of Science and Technology (POSTECH) (Korea, Republic of)
Argonne National Laboratory (ANL), Argonne, IL (United States)
Pohang Univ. of Science and Technology (POSTECH) (Korea, Republic of); Kookmin Univ., Seoul (Korea, Republic of)

Cyanase plays a vital role in the detoxification of cyanate and supplies a continuous nitrogen source for soil microbes by converting cyanate to ammonia and carbon dioxide in a bicarbonate-dependent reaction. The structures of cyanase complexed with dianion inhibitors, in conjunction with biochemical studies, suggest putative binding sites for substrates. However, the substrate-recognition and reaction mechanisms of cyanase remain unclear. Here, crystal structures of cyanase from Escherichia coli were determined in the native form and in complexes with cyanate, bicarbonate and intermediates at 1.5–1.9 Å resolution using synchrotron X-rays and an X-ray free-electron laser. Cyanate and bicarbonate interact with the highly conserved Arg96, Ser122 and Ala123 in the active site. Further, in the presence of a mixture of cyanate and bicarbonate, three different electron densities for intermediates were observed in the cyanase structures. Moreover, the observed electron density could explain the dynamics of the substrate or product. In addition to conformational changes in the substrate-binding pocket, dynamic movement of Leu151 was observed, which functions as a gate for the passage of substrates or products. These findings provide a structural mechanism for the substrate-binding and reaction process of cyanase.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: Korea Institute of Science and Technology Information; National Research Foundation of Korea (NRF)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 2566861

Journal Information:: Acta Crystallographica. Section D. Structural Biology, Journal Name: Acta Crystallographica. Section D. Structural Biology Journal Issue: 12 Vol. 79; ISSN 2059-7983

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Escherichia coli
X-ray free-electron lasers
cyanase
gating mechanisms
intermediate strutures
substrate recognition

Structural mechanism of Escherichia coli cyanase

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