2DPX

Crystal Structure of human Rad GTPase

Summary for 2DPX

• Entry DOI: 10.2210/pdb2dpx/pdb
• Descriptor: GTP-binding protein RAD, MAGNESIUM ION, GUANOSINE-5'-DIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: rad, gtpase, small-g, rgk, signal transduction, diabetes, signaling protein
• Biological source: Homo sapiens (human)
• Cellular location: Cell membrane (By similarity): P55042
• Total number of polymer chains: 2
• Total formula weight: 39036.06

Authors

Yanuar, A.,Sakurai, S.,Kitano, K.,Hakoshima, T. (deposition date: 2006-05-18, release date: 2006-08-08, Last modification date: 2023-10-25)

Primary citation

Yanuar, A.,Sakurai, S.,Kitano, K.,Hakoshima, T.
Crystal structure of human Rad GTPase of the RGK-family
Genes Cells, 11:961-968, 2006

PubMed Abstract: Rad (Ras associated with diabetes) is an RGK-family small GTPase that is over-expressed in the skeletal muscle of humans with type II diabetes. Unlike other small GTPases, RGK family members including Rad lack several conserved residues in the GTPase domain. Here, we report the crystal structure of the GTPase domain of human Rad in the GDP-bound form at 1.8 A resolution. The structure revealed unexpected disordered structures of both switches I and II. We showed that the conformational flexibility of both switches is caused by non-conservative substitutions in the G2 and G3 motifs forming the switch cores together with other substitutions in the structural elements interacting with the switches. Glycine-rich sequences of the switches would also contribute to the flexibility. Switch I lacks the conserved phenylalanine that makes non-polar interactions with the guanine base in H-Ras. Instead, water-mediated hydrogen bonding interactions were observed in Rad. The GDP molecule is located at the same position as in H-Ras and adopts a similar conformation as that bound in H-Ras. This similarity seems to be endowed by the conserved hydrogen bonding interactions with the guanine base-recognition loops and the magnesium ion that has a typical octahedral coordination shell identical to that in H-Ras.

PubMed: 16866878
DOI: 10.1111/j.1365-2443.2006.00994.x

Experimental method

X-RAY DIFFRACTION (1.8 Å)