PDBsum entry 1am4

Complex (gtpase-activating/gtp-binding)

PDB id: 1am4

Contents

Protein chains

199 a.a. *

174 a.a. *

Ligands

GNP ×3

Metals

_MG ×3

Waters ×302

* Residue conservation analysis

PDB id:

1am4

Name:

Complex (gtpase-activating/gtp-binding)

Title:

Complex between cdc42hs.Gmppnp and p50 rhogap (h. Sapiens)

Structure:

P50-rhogap. Chain: a, b, c. Engineered: yes. Cdc42hs. Chain: d, e, f. Engineered: yes. Mutation: yes. Other_details: heterodimer

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cellular_location: cytoplasm. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å R-factor: 0.230 R-free: 0.280

Authors:

K.Rittinger,P.Walker,S.J.Gamblin,S.J.Smerdon

Key ref:

K.Rittinger et al. (1997). Crystal structure of a small G protein in complex with the GTPase-activating protein rhoGAP. Nature, 388, 693-697. PubMed id: 9262406 DOI: 10.1038/41805

Date:

22-Jun-97 Release date: 15-Jul-98

Protein chains

Q07960  (RHG01_HUMAN) -  Rho GTPase-activating protein 1 from Homo sapiens

Seq: 439 a.a.

Struc: 199 a.a.

Protein chains

P60953  (CDC42_HUMAN) -  Cell division control protein 42 homolog from Homo sapiens

Seq: 191 a.a.

Struc: 174 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, B, C: E.C.?
• Enzyme class 3: Chains D, E, F: E.C.3.6.5.2 - small monomeric GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

GTP + H2O = GDP (Bound ligand (Het Group name = GNP) matches with 81.82% similarity) + phosphate + H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/41805

Nature 388:693-697 (1997)

PubMed id: 9262406

Crystal structure of a small G protein in complex with the GTPase-activating protein rhoGAP.

K.Rittinger, P.A.Walker, J.F.Eccleston, K.Nurmahomed, D.Owen, E.Laue, S.J.Gamblin, S.J.Smerdon.

ABSTRACT

Small G proteins transduce signals from plasma-membrane receptors to control a wide range of cellular functions. These proteins are clustered into distinct families but all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of G proteins, which includes Cdc42Hs, activate effectors involved in the regulation of cytoskeleton formation, cell proliferation and the JNK signalling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GTPase-activating proteins (GAPs) that enhance the rate of GTP hydrolysis by up to 10(5) times. We report here the crystal structure of Cdc42Hs, with the non-hydrolysable GTP analogue GMPPNP, in complex with the GAP domain of p50rhoGAP at 2.7A resolution. In the complex Cdc42Hs interacts, mainly through its switch I and II regions, with a shallow pocket on rhoGAP which is lined with conserved residues. Arg 85 of rhoGAP interacts with the P-loop of Cdc42Hs, but from biochemical data and by analogy with the G-protein subunit G(i alpha1), we propose that it adopts a different conformation during the catalytic cycle which enables it to stabilize the transition state of the GTP-hydrolysis reaction.

Selected figure(s)

Figure 1.
Figure 1 a, The structure of the Cdc42Hs GMPPNP/p50rhoGAP complex viewed along the protein-protein interface. Cdc42Hs is coloured green, with the conserved switch I (residues 32 to 40), switch II (residues 60 to 67) and P-loop (residues 10 to 17) regions in red. These bind to a shallow depression in rhoGAP (blue) formed by the A-Al loop and helices B and F which are highlighted in magenta. Formation of the complex buries 1,807 ring 2of accessible surface, of which 61% (1,115 ring 2) is made up of non-polar side-chain atoms. The C positions of Arg 85[r] and Tyr 64[c] are highlighted. b, Stereo view of the interactions between Cdc42Hs and p50rhoGAP viewed from the same direction as in a. Secondary-structure elements of Cdc42Hs and rhoGAP are coloured green and blue respectively, with Cdc42Hs side chains in grey and those of rhoGAP in yellow. In both cases, oxygen and nitrogen atoms are red and blue respectively. The electron density for residues 29-31 of the switch I region of Cdc42Hs is poor. Electron density for Tyr 32[c] is relatively poor at the current state of refinement, but it does refine adequately in a conformation which makes additional contacts with Lys 189[r], Thr 191[r] and Asn 194[r], Arg 85[r] occupies a conformation close to the P-loop of Cdc42Hs and interacts either through direct hydrogen bonding with the C=O of Gly 12[c] or through water mediated contacts. Gln61[c], which is important in the GTP hydrolysis reaction, is disordered in this structure as it is in X-ray structures of Ras. (Panels a and b were produced using MOLSCRIPT29.)

Figure 3.
Figure 3 Comparison of the Cdc42Hs GMPPNP/p50rhoGAP complex with the structure of transducin- GTP S. Here, Cdc42Hs is shown in blue, with rhoGAP in red and transducin- in white. Transducin- consists of two domains: one is structurally homologous to the small GTPase family and the other is a smaller -helical domain unique to the heterotrimeric G-protein family. Least-squares overlap28 of Cdc42Hs with the GTPase domain of transducin gives an r.m.s. fit of 1.7 ring for 122 structurally equivalent C atoms. Arg 174 has been proposed to be involved in transition-state stabilization during GTP hydrolysis in transducin. Its C position is shown in yellow and is positioned within a piece of extended structure corresponding to the effector or switch I region of Cdc42Hs (magenta). In contrast, Arg 85[r], which appears to fulfil a similar role in GTPase activation by p50rhoGAP, is situated on the A-Al loop on the opposing face of the triphosphate moiety of the nucleotide analogue.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1997, 388, 693-697) copyright 1997.

Figures were selected by an automated process.