Interface Analysis of Small GTP Binding Protein Complexes Suggests Preferred Membrane Orientations
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Biol. Chem. 2017; 398(5-6): 637–651 Review Open Access Ingrid R. Vetter* Interface analysis of small GTP binding protein complexes suggests preferred membrane orientations DOI 10.1515/hsz-2016-0287 N-terminal glycine (Arf family, myristoylation) or at the Received September 16, 2016; accepted December 12, 2016; C-terminal CAAX box (Ras, Rho, Rab families, farnesylation previously published online December 21, 2016 or geranylgeranylation). Some G proteins are additionally modified by palmitoyl groups at cysteines preceding the Abstract: Crystal structures of small GTP binding protein CAAX box (e.g. H-Ras, N-Ras, K-Ras4A, Rap2A-B), whereas complexes with their effectors and regulators reveal that in others the palmitoylation site is replaced by a polyba- one particularly flat side of the G domain that contains sic stretch (e.g. K-Ras4B, Rap1) (Colicelli, 2004; Tsai et al., helix α4 and the C-terminal helix α5 is practically devoid 2015). As the prenyl groups are irreversibly attached, the of contacts. Although this observation seems trivial as membrane affinity conferred by those groups can be regu- the main binding targets are the switch I and II regions lated only by helper proteins that bind to and shield the opposite of this side, the fact that all interacting proteins, prenyl group from solvent, like the GDI-type proteins. In even the largest ones, seem to avoid occupying this area contrast, the palmitoyl groups are reversibly attached by (except for Ran, that does not localize to membranes) is DHHC proteins at the Golgi apparatus and can be removed very striking. An orientation with this ‘flat’ side parallel by thioesterases. Candidate human thioesterases are APT1 to the membrane was proposed before and would allow and APT2 (Görmer et al., 2012). The closely related human simultaneous interaction of the lipidated C-terminus and protein LYPLAL1 has been shown to be unable to cleave positive charges in the α4 helix with the membrane while palmitoyl chains (Bürger et al., 2012). The involvement being bound to effector or regulator molecules. Further- of APTs in depalmitoylation is unclear, e.g. the ortholo- more, this ‘flat’ side might be involved in regulatory mech- gous protein to APT1/APT2 in toxoplasma can be knocked anisms: a Ras dimer that is found in different crystal forms out without major consequences (Kemp et al., 2013), and interacts exactly at this side. Additional interface analysis APT1/2 inhibition/knockdown did not show a significant of GTPase complexes nicely confirms the effect of different effect on N-Ras localization in NRAS mutant melanoma flexibilities of the GTP and GDP forms. Besides Ran pro- cells (Vujic et al., 2016), but inhibition of APTs (Rusch teins, guanine nucleotide exchange factors (GEFs) bury et al., 2011; Zimmermann et al., 2013) indeed altered Ras the largest surface areas to provide the binding energy to localization (Dekker et al., 2010). Efforts to exploit the open up the switch regions for nucleotide exchange. palmitoylation machinery for therapeutic purposes are Keywords: buried interface; crystal structures; effector ongoing (Cox et al., 2015). Recently, other candidates complexes; G domain dimerization; GTPase; membrane for palmitoyl cleavage have been proposed, the ABDH17 interaction. family proteins (Lin and Conibear, 2015), and more might be found since the serine hydrolase family has many uncharacterized members. Introduction From a structural viewpoint, the G domain (GTP binding domain) of the family of small GTP binding pro- Most small GTP binding proteins except Ran are post- teins is a versatile module that has evolved from an ances- translationally modified with prenyl groups at either an tral fold, the P-loop containing nucleoside triphosphate binding domain (Leipe et al., 2002; Ma et al., 2008). This fold is characterized by the presence of more or less flex- *Corresponding author: Ingrid R. Vetter, Max Planck Institute of Molecular Physiology, Department of Mechanistic Cell Biology, ible molecular ‘switch’ regions. According to the ‘loaded Otto-Hahn-Str. 11, D-44227 Dortmund, Germany, spring’ hypothesis (Vetter and Wittinghofer, 2001) the e-mail: [email protected] two switch regions are restrained in their dynamics by ©2017, Ingrid R. Vetter, published by De Gruyter. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. 638 I.R. Vetter: Interface analysis of GTP binding protein complexes the γ-phosphate of a GTP molecule, so that the entropic Post-translational modifications penalty for binding of effector molecules and GTPase acti- vating proteins (GAPs) especially to the switch I region is and other structural determinants decreased. Consequentially, GDP binding increases the of membrane orientation flexibility of the switches and attracts different interaction partners, the nucleotide exchange factors (GEFs) and the In the available crystal structures of small GTP binding guanine nucleotide dissociation inhibitors (GDIs), using proteins, the C-terminal hydrophobic modifications are different additional contact regions. rarely present as they render the proteins very poorly The functionality of the G domain has expanded soluble. Thus, prenylated GTPases usually crystallize during evolution by introduction of various insertions only in complex with GDI proteins that chaperone the (Wittinghofer and Vetter, 2011). The Rho/Rac/Cdc42 family hydrophobic group, like the RabGDI Ypt1 (1UKV; Rak has a small insertion of approx. 13 residues forming a et al., 2003), RhoGDIs [(1DOA; Hoffman et al., 2000), short α-helix between helix α4 and β-strand β4 that does 1HH4 (Grizot et al., 2001), 4F38 (Tnimov et al., 2012), not change the conformation upon nucleotide hydrolysis 5FR2; Kuhlmann et al., 2016)], PDE6δ (3T5G; Ismail et al., and is usually not directly involved in effector binding. 2011) or REP (Rab escort protein, 1VG0; Rak et al., 2004). Arf/Arl/Sar proteins undergo a large conformational The lipid modification site is separated from the G domain change of the G domain core where a register change of by a hypervariable region (HVR, 167-189, Figure 1B) that is two β-strands causes the N-terminus, usually an amphi- assumed to be flexible and is normally deleted for crys- philic, myristoylated helix, to detach from the protein core tallization, so that there are only a few crystal structures (therefore called ‘N-terminal switch’) so that it can inter- of full-length GTPases. For Ras proteins, one structure is act with membranes or effectors (Pasqualato et al., 2002; H-Ras-GDP 1-189 (4Q21; Milburn et al., 1990); the second Gillingham and Munro, 2007). Ran GTPases have an addi- one is K-Ras4B 1-189 (GDP, 4DSU, GSP, 4DSO; Maurer tional C-terminal helix that is destabilized if GTP is bound et al., 2012). In the H-Ras structure (4Q21), the C-terminal (called ‘C-terminal switch’; Vetter et al., 1999b). helix (α5) is visible up to Leu168, so this structure does Summaries of the structural features of G domain con- not contribute much additional information compared taining proteins can be found in the following references: to the truncated structures (usually comprising residues Vetter and Wittinghofer (1999), Paduch et al. (2001), Cher- 1-166). In the K-Ras structures (4DSU, 4DSO), the C-ter- fils and Zeghouf (2011), Wittinghofer and Vetter (2011) and minal helix continues up to residue Asp173, which is the Vetter (2014). In the following, structural characteristics of last residue with unambiguous electron density (Maurer complexes of small GTP binding proteins are highlighted, et al., 2012). The remaining residues 174–180 that contain with a focus on the implications for orientation at the the polybasic region, mostly lysines, have only weak membrane. electron density, indicating their intrinsic flexibility, and Membrane Membrane 47 161 161 C 128 135 172 180 165 135 128 165 169 N N 175 KKKKKK motif of K-Ras AB Figure 1: Proposed interaction of the three Ras proteins with the plasma membrane (orange). H-Ras in gray (5P21, GppNHp-bound), K-Ras in blue (4DSU, GDP-bound, 4DSO, GSP-bound, both look very similar), N-Ras in violet (GDP-bound, 3CON). (A) Positions carrying positive charges (128, 135, 161) are labeled and side chains shown as sticks, and residue 47 of the β-hairpin loop is indicated. (B) Orientation 110° rotated compared to (A). The hypervariable region (residues 167–189) forms an α-helix for residues 167–174 in the K-Ras structure (blue) and is probably flexible after residue 174, thus, the lysine side chains of the polybasic region were modeled according to geometrical constraints. I.R. Vetter: Interface analysis of GTP binding protein complexes 639 are assumed to facilitate the interaction with the nega- position corresponding to Ras R161, but positions 128 and tively charged lipid head groups of membranes (Figure 135 are not conserved (at 128, e.g. R,K,E,Q,D, at position 1B) (Maurer et al., 2012). The farnesylated cysteine of the 135, e.g. R,K,D,Y). In the Rho family, positions correspond- CAAX box follows shortly after the positively charged ing to R161 and R135 in Ras are conserved as R/K, but posi- region at residue 185 (CVIM). Many Rho family GTPases tion 128 has no positive charge, but is often E,Q or D. In have a similar HVR compared to Ras (Vidal, 2010) in Arf proteins, position 135 is mostly histidine, but the other terms of length and (positive) charges. Rab proteins two positions often have negative charges. A summary of tend to have a C-terminal helix that is longer than in the charge distributions in helices α4 and α5 can be found Ras protein structures [e.g. up to 13 residues in Rab11A in a recent review (Prakash and Gorfe, 2016). In addition, (3BFK, unpublished), Rab11B (2F9M; Scapin et al., 2006) Arf proteins, the major traffic regulators in the cell besides and Rab7 (1VG8; Rak et al., 2004)], and Rab proteins Ran and Rab proteins, have their lipid modification at the also have a longer linker between the helix end and the N-terminus instead of the C-terminus, and therefore will lipid modification site.