cdc42: cell division control homolog 42
Analysis of Conserved Domains
Various conserved domains in cdc42 have been found and examined using the NCBI conserved domains search. They are highlighted on the MultAlin sequence in green.
Go to various conserved domains by clicking on the buttons below:
GTP/Mg2+ binding site
Mg2+, when associated with this domain, plays a key role in bringing together the functional regions of the GDP/GTP-binding site, the Switch I and the Switch II. Mg2+ also has a direct role in regulating the kinetics of the GEF- and GAP-catalysed reactions of guanine-nucleotide-associated Cdc42. When GDP is associated with this domain with its Mg2+, Cdc42 is in its inactive conformation, but when GTP is bound, it changes into its active conformation.
GAP interaction site
GTPase Activating Protein (GAP) interaction site. This is a binding site for GAP. GAPs bind to G-proteins and upregulate GTPase activity, which breaks the phosphate bond in GTP making GDP. If G-proteins are bound to GDP they are turned ‘off’, so this effectively ends any signalling by cdc42. This is highly important in cdc42’s role as a regulatory G-protein.
GEF interaction site
GEFs (guanine-nucleotide exchange factors) interact with this domain by inserting an alpha-helix into inactive Cdc42 that displaces the Switch I region, which opens up the nucleotide binding site. Side chains on the alpha-helix disturb the chemical environment around the bound Mg2+ and GDP in the Cdc42 protein, causing their association to become unfavourable. The GEF stabilises the Cdc42 into an open conformation that mimics its conformation when it is bound to GTP instead of GDP, consequently causing the Cdc42 to release GDP and take up GTP in an exchange, making the Cdc42 conformationally active.
GDI interaction site
A GDI (guanine-nucleotide dissociation inhibitor) interacts with this region by binding to in when Cdc42 is in its GDP-bound, inactive form. This bond prevents GEFs from exchanging GDP for GTP, thus keeping Cdc42 in its inactive form. The GDI can be removed with a GDI displacement factor (GDF) that returns Cdc42’s ability to become active.
CRIB effector interaction site
The CRIB (Cdc42/Rac-interactive binding) domain interacts with various effector proteins in the multiple cell-signalling cascades that Cdc42 is involved in. In one cascade, the active Cdc42 attaches to an inactive effector protein, making it active. The Cdc42-effector complex then activates another protein, thus continuing the cascade. The cascade will eventually result in a distinct phenomenon, be that changes in cell morphology, increase in cell motility or some other related process.
Par6 cell polarity protein interaction site
Activated by cdc42 which organises cell polarity through the cell cytoskeleton in developing organisms.
ACK tyrosine kinase interaction site
Activated Cdc42-associated tyrosine Kinase (ACK). ACK is activated in response to certain cellular signals. It binds to cdc42 through the GTPase binding domain of ACK and the ACK tyrosine kinase interaction site on cdc42. Relatively little information on its role in the signalling process, however it could inhibit cdc42 as with GDI or upregulate cdc42 as with GEF.
Switch I region
One of two surface loops that undergo conformational changes upon GDP/GTP binding, and that play key roles in GEF and GAP binding.
Switch II region
The second surface loop region.
G1 box
Characterised by [aaaaGxxxxGKS/T], where a is L/I/V/M and x is any amino acid. Also known as P-loop/Walker A motif. Purine nucleotide binding signature.
G2 box
G2 box motif is characterized by threonine (T or Thr) conservation within Ras-like superfamily of GTPases. Neighbouring residues are conserved within protein subfamilies.
G3 box
Characteristic G3 box motif consists of Aspartic acid (D) - x - x - Glycine (G) stretch with x being any amino acid. Aspartic acid residue is highly conserved even in Ras-like superfamily and it is involved in binding a nucleotide-associated Mg2+ ion.
G4 box
G4 box motif consists of Asparagine (N) or Threonine (T) - Lysine (K) or Glutamine (Q) - x - Aspartic Acid (D) with x being any amino acid. G4 box residues make hydrogen bonds with the guanine ring (giving specificity to GTP over ATP) and make stabilizing interactions with G1 box motif amino acids.
G5 box
The most conserved amino acids in G5 box are Serine (S) - Alanine (A) - Lysine (K) or Leucine (L). They make indirect contact with the guanine nucleotide.
References:
National Center for Biotechnology Information website: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi
John Colicelli (2004), Human RAS Superfamily Proteins and Related GTPases, Sci STKE
------------
http://www.ncbi.nlm.nih.gov/pubmed/22553920
Lin, Q., Wang, J., Childress, C., Yang, W. (2012) 'The activation mechanism of ACK1 (activated Cdc42-associated tyrosine kinase 1).', Biochemical Journal, 445(2), pp. 255-264.
------------