Human OLA1 Defines an ATPase Subfamily in the Obg Family of GTP-binding Proteins

Roland Koller-Eichhorn,Tobias Marquardt,Robert Gail,Alfred Wittinghofer,Dirk Kostrewa,Ulrike Kutay,Christian Kambach

doi:10.1074/jbc.m700541200

Roland Koller-Eichhorn, Tobias Marquardt + Show 5 more

Open Access

https://doi.org/10.1074/jbc.m700541200

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Abstract

Purine nucleotide-binding proteins build the large family of P-loop GTPases and related ATPases, which perform essential functions in all kingdoms of life. The Obg family comprises a group of ancient GTPases belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies. The founding member of one of these subfamilies is the bacterial P-loop NTPase YchF, which had so far been assumed to act as GTPase. We have biochemically characterized the human homologue of YchF and found that it binds and hydrolyzes ATP more efficiently than GTP. For this reason, we have termed the protein hOLA1, for human Obg-like ATPase 1. Further biochemical characterization of YchF proteins from different species revealed that ATPase activity is a general but previously missed feature of the YchF subfamily of Obg-like GTPases. To explain ATP specificity of hOLA1, we have solved the x-ray structure of hOLA1 bound to the nonhydrolyzable ATP analogue AMPPCP. Our structural data help to explain the altered nucleotide specificity of YchF homologues and identify the Ola1/YchF subfamily of the Obg-related NTPases as an exceptional example of a single protein subfamily, which has evolved altered nucleotide specificity within a distinct protein family of GTPases.

Highlights

Molecular switches such that the GTP-bound form constitutes the active state and triggers the biological output whereas the GDP-bound form is inactive
The G2 (X(T/S)X) and G3/Walker B motifs are involved in the coordination of a Mg2ϩ ion that is required for nucleotide binding and hydrolysis
The switch I and II regions interact with the ␥-phosphate of the bound GTP, resulting in a protein conformation that is highly responsive to GTP hydrolysis and loss of the ␥-phosphate

Summary

EXPERIMENTAL PROCEDURES

Phylogenetic Tree Construction and Sequence Alignment— Phylogenetic distribution and multiple sequence alignment of Obg-like proteins were calculated with ClustalW (www.ebi.ac.uk/clustalw) and displayed using TreeView [15] or JalView. Peak fractions were pooled and concentrated by Centricon centrifugation (Milian) prior to gel filtration on a Superdex 200 10/30 column (GE Healthcare) in 50 mM Tris, pH 7.6, 100 mM NaCl, 5 mM MgCl2. Nucleotide Hydrolysis Assay—To quantify nucleotide hydrolysis, 5 ␮M protein was incubated with an excess of either ATP or GTP (125 ␮M) in 50 mM Tris, pH 7.6, 200 mM NaCl, 5 mM MgCl2 at 25 °C. Modeling of the cofactor AMPPCP was performed by superposition of the putative nucleotide-binding site of hOLA1 with that of GTP-bound p21-H-Ras (Protein Data Bank code 121P; [24]), using the position and conformation of GTP as a starting point. Core root mean square deviation (RMSD) values are in Angstroms

RESULTS

Ramachandran plot

DISCUSSION

YchF behave similarly to the related