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Crystal structure of the GDP-bound GTPase domain of Rab5a from Leishmania donovani

Zohib, Muhammad; Maheshwari, Diva; Pal, Ravi Kant; Freitag-Pohl, Stefanie; Biswal, Bichitra Kumar; Pohl, Ehmke; Arora, Ashish

Crystal structure of the GDP-bound GTPase domain of Rab5a from Leishmania donovani Thumbnail


Muhammad Zohib

Diva Maheshwari

Ravi Kant Pal

Stefanie Freitag-Pohl

Bichitra Kumar Biswal

Ashish Arora


Eukaryotic Rab5s are highly conserved small GTPase-family proteins that are involved in the regulation of early endocytosis. Leishmania donovani Rab5a regulates the sorting of early endosomes that are involved in the uptake of essential nutrients through fluid-phase endocytosis. Here, the 1.80 Å resolution crystal structure of the N-terminal GTPase domain of L. donovani Rab5a in complex with GDP is presented. The crystal structure determination was enabled by the design of specific single-site mutations and two deletions that were made to stabilize the protein for previous NMR studies. The structure of LdRab5a shows the canonical GTPase fold, with a six-stranded central mixed β-sheet surrounded by five α-helices. The positions of the Switch I and Switch II loops confirm an open conformation, as expected in the absence of the γ-phosphate. However, in comparison to other GTP-bound and GDP-bound homologous proteins, the Switch I region traces a unique disposition in LdRab5a. One magnesium ion is bound to the protein at the GTP-binding site. Molecular-dynamics simulations indicate that the GDP-bound structure exhibits higher stability than the apo structure. The GDP-bound LdRab5a structure presented here will aid in efforts to unravel its interactions with its regulators, including the guanine nucleotide-exchange factor, and will lay the foundation for a structure-based search for specific inhibitors


Zohib, M., Maheshwari, D., Pal, R. K., Freitag-Pohl, S., Biswal, B. K., Pohl, E., & Arora, A. (2020). Crystal structure of the GDP-bound GTPase domain of Rab5a from Leishmania donovani. Acta Crystallographica Section F: Structural Biology Communications, 76(11), 544-556.

Journal Article Type Article
Acceptance Date Oct 13, 2020
Publication Date 2020-11
Deposit Date Nov 19, 2020
Publicly Available Date Nov 19, 2020
Journal Acta Crystallographica Section F: Structural Biology Communications
Publisher International Union of Crystallography
Peer Reviewed Peer Reviewed
Volume 76
Issue 11
Pages 544-556


Accepted Journal Article (Electronic reprint) (1.9 Mb)

Copyright Statement
Electronic reprint

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