Guanine nucleotide binding proteins

  1. Introduction to guanine nucleotide binding proteins
  2. Structure of small guaning nucleotide binding proteins, p21Ras
  3. Conformational change between on and off states
  4. References
  5. PDB 3D structure files from Brookhaven National Laboratory


Guanine nucleotide binding proteins are glycoproteins anchored on the cytoplasmic cell membrane. They are mediators for many cellular processes, including signal transduction, protein transport, growth regulation and polypeptide chain elongation. They are also known as GTP-binding proteins and GTPases. Almost all members of this superfamily of proteins act as molecular switch, which is on when GTP is bound and off when GDP is bound. Binding is specific for the guanine base, with affinity of the order of 1011-1012 M-1 for GDP and GTP, whilst binding affinity for GMP and other nucleotide bases are 6 orders less.

The activity of guanine nucleotide binding proteins is dependent on divalent ions, which is Mg++ in vivo. Mg++ forms octahedral coordinate bonds. When GTP is bound, two neighbouring equatorial dative bonds are connected to 2 oxygen atoms of the beta and gamma phosphates of GTP, whilst the other two equatorial bonds are connected to the hydroxyl oxygen of Ser17 and Thr35, respectively. Both polar dative bonds are linked to water molecules. When GDP is bound, the coordinately bonded oxygen of gamma phosphate is replaced by a water molecule. The hydroxyl oxygen of Thr35 is also broken off and replaced by a water molecule.

Structure of p21Hras

Ras proteins are divided into two domains, G domain which is the guanine nucleotide binding region, and the C domain which anchors the protein onto the cytoplasmic side of the cell membrane. Ras proteins belongs to the alpha/beta class of proteins, with the G domain made of a central beta sheet of 6 strands, flanked below by 2 alpha helices and above by 3 alpha helices. These are connected by turns and loops. Loops 1, 2 and 4 are of crucial importance as they surround the active centre at the gamma phosphate group of bound GTP.

5P21 shows guanosine-5'-(beta, gamma-imido)triphosphate bound to the G domain of p21Hras. Caged GTP or analogues are used for crystallographic studies as GTP is hydrolysed during crystallisation. Mg++ is shown as a green ball. GppNp is shown in ball and stick with CPK colouring. Loops 1, 2 and 4 are shown in violet, magenta and purple colours respectively. These three loops surround the active centre containing GTP and Mg++.

Conformational change between the active and inactive forms of p21Hras

GTP-bound p21Hras mediate cellular responses by acting on its effector molecules, like phospholipases C and A2 and adenylyl cyclase. This activity is tightly regulated by hydrolysis of bound GTP into GDP which is subsequently released from the G protein. The GTPase activity may be intrinsic or due to the action of effector molecules. GTPase activity is stimulated by GTPase activiating protein(GAP). The markedly different action of the G proteins on and off state is structurally related to its conformational change between the two states. In the GTP-bound on state, loops 2 and 4 of the G protein are tied into a connected loop conformation by the gamma phosphate of GTP. The connection is strengthened with Thr35 of loop 2 coordinated to Mg++ ion which also coordinates to both the beta and gamma phosphates of GTP.

Loops 2 and 4 connection is effected by Thr35 of loop 2 and Gly60 of loop 4 interacting with GppNp. The amide groups of Thr35 and Gly60 form hydrogen bonds with 2 oxygen atoms of the gamma phosphate, thus connecting the loops together. Thr35 is also coordinated to Mg++ through its OH group.
The following two diagrams illustrate the close contacts that allow the hydrogen bons to connect the two loops.

GppNp, Mg, Thr35 and Gly60 in spacefill model to show the close contact of gamma PO4 of GppNp with the other three molecules.

Whole complex in spacefill model to confirm the close contact of gamma PO4 of GppNp with the Thr35 and Gly60.

When the gamma phosphate is cleaved by nucleophilic attack by water, loops 2 and 4 are disconnected from each other. Thr35 and loop 2 is also released from coordination by Mg++ ion. The two loops reorientate themselves in the GDP-bound state.
The reorientations of loops 2 and 4 are shown in the following diagrams

Loops in ribbon model to depict the reorientations.

GDP, Thr35 and Gly60 in spacefill model to show that Thr35 and Gly60 are no longer in close contact with GDP.

Whole complex in spacefill model emphasising that Thr35 and Gly60 are no longer in close contact with GDP.

The effect of this conformational change on the action of guanine nucleotide binding proteins on the effector molecules is unknown because of the lack of knowledge on the mechanism of interaction between guanine nucleotide binding proteins and effectors. This is despite a lot of speculation on the role of GTPase and GAP as effector molecules.
Much more is known concerning the effect of the conformational change on the GTPase activity. The gamma phosphate is cleaved by nucleophilic attack by a water molecule. This nucleophilic attack is assisted when the water molecule is strongly polarised by forming hydrogen bonds. In the GTP-bound conformation, Gln61 in loop 4 is in the favourable position for its side chain carbonyl oxygen to form hydrogen bond with the attacking water molecule. This polarising effect on the nucleophilic water attacker is further assisted by hydrogen bonding with the main chain carbonyl oxygen of Thr35 in loop 2, which is favourably oriented in the GTP-bound conformation. After the gamma phosphate is cleaved off by the GTPase, loops 2 and 4 lose their grip on GDP and reorientate themselves. They are no longer in the favourable positions to polarise the attacking water nucleophile.


  1. Wittinghofer A. Three-dimensional structure of p21H-ras and its implications. Cancer Biology 3:189-198, 1992.
  2. Wittinghofer A et al. Three-dimensional structure and properties of wild-type and mutant H-ras-encoded p21. CIBA Foundation Symposium 176:6-21, 1993.
  3. Pai EF et al. Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 Angstrom resolution: implications for the mechanism of GTP hydrolysis.

PDB structure files

  1. 5P21- wild p21Hras G domain complexed with GppNp.
  2. 4Q21- wild p21Hras G domain complexed with GDP.
  3. Wild p21Hras G domains complexed with other GTP analogues- 1GNP, 1GNR.
  4. Other mutant p21Hras G domains- 2021, 521P, 821P, 1PLL, 1PLK, 1PLJ, 721P.