The glycine brace: a component of Rab, Rho, and Ran GTPases associated with hinge regions of guanine- and phosphate-binding loops

Bayesian analysis of divergent patterns within a multiple alignment of Ras-like GTPase sequences identifies a structural component, termed here the glycine brace, as the feature that most distinguishes Rab, Rho/Rac, Ran and (to some degree) Ras family GTPases from other Ras-like GTPases. The glycine brace consists of four residues: An aromatic residue that forms a stabilizing CH-π interaction with a conserved glycine at the start of the guanine-binding loop; a second aromatic residue, which is nearly always a tryptophan, that likewise forms stabilizing CH-π and NH-π interactions with a glycine at the start of the phosphate-binding P-loop; and two other residues (typically an aspartate and a serine or threonine) that, together with a conserved buried water molecule, form a network of interactions connecting the two aromatic residues.It is proposed that the two glycine residues function as hinges and that the glycine brace influences guanine nucleotide binding and release by interacting with these hinges.Rab [1], Rho/Rac [2] and Ran [3,4] GTPases regulate diverse cellular processes including vesicle trafficking, cytoskeletal dynamics, cell polarity, membrane fusion, chromosome segregation, and nuclear transport. These proteins are a subgroup of the extended Ras-like superfamily of GTPases [5] (termed here the Ras-like GTPases), which function as signaling pathway on-off switches and which also include Arf, Arf-like (Arl), and Sar GTPases and α subunits of heterotrimeric G proteins. Given an appropriate upstream signal, Ras-like GTPases are turned 'on' by binding to GTP, resulting in their association with various 'effectors' that propagate the incoming signal to downstream components. Guanine nucleotide exchange factors (GEFs) facilitate this process by mediating the exchange of GTP for GDP. Ras-like GTPases are turned off upon hydrolysis of GTP to GDP, which results in termination of the signal and a shutting off of the pathway. GTPase activating proteins (GAPs) faci