PDBsum entry 1ki1

Signaling protein

PDB id: 1ki1

Contents

Protein chains

178 a.a. *

342 a.a. *

Ligands

SO4 ×2

Waters ×181

* Residue conservation analysis

PDB id:

1ki1

Name:

Signaling protein

Title:

Guanine nucleotide exchange region of intersectin in complex with cdc42

Structure:

G25k gtp-binding protein, placental isoform. Chain: a, c. Fragment: residues 1-188. Synonym: cdc42. Engineered: yes. Mutation: yes. Intersectin long form. Chain: b, d. Fragment: dbl homology and pleckstrin homology domains (residues

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.231 R-free: 0.247

Authors:

J.T.Snyder,W.M.Pruitt,C.J.Der,J.Sondek

Key ref:

J.T.Snyder et al. (2002). Structural basis for the selective activation of Rho GTPases by Dbl exchange factors. Nat Struct Biol, 9, 468-475. PubMed id: 12006984 DOI: 10.1038/nsb796

Date:

02-Dec-01 Release date: 29-May-02

Protein chains

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

Seq: 191 a.a.

Struc: 178 a.a.

Protein chains

Q15811  (ITSN1_HUMAN) -  Intersectin-1 from Homo sapiens

Seq: 1721 a.a.

Struc: 342 a.a.*

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

Enzyme reactions

• Enzyme class: Chains A, C: E.C.3.6.5.2 - small monomeric GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

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

reference

DOI no: 10.1038/nsb796

Nat Struct Biol 9:468-475 (2002)

PubMed id: 12006984

Structural basis for the selective activation of Rho GTPases by Dbl exchange factors.

J.T.Snyder, D.K.Worthylake, K.L.Rossman, L.Betts, W.M.Pruitt, D.P.Siderovski, C.J.Der, J.Sondek.

ABSTRACT

Activation of Rho-family GTPases involves the removal of bound GDP and the subsequent loading of GTP, all catalyzed by guanine nucleotide exchange factors (GEFs) of the Dbl-family. Despite high sequence conservation among Rho GTPases, Dbl proteins possess a wide spectrum of discriminatory potentials for Rho-family members. To rationalize this specificity, we have determined crystal structures of the conserved, catalytic fragments (Dbl and pleckstrin homology domains) of the exchange factors intersectin and Dbs in complex with their cognate GTPases, Cdc42 and RhoA, respectively. Structure-based mutagenesis of intersectin and Dbs reveals the key determinants responsible for promoting exchange activity in Cdc42, Rac1 and RhoA. These findings provide critical insight into the structural features necessary for the proper pairing of Dbl-exchange factors with Rho GTPases and now allow for the detailed manipulation of signaling pathways mediated by these oncoproteins in vivo.

Selected figure(s)

Figure 1.
Figure 1. Overall structures of ITSN -Cdc42 and Dbs -RhoA. a, Stereo view of an electron density map calculated using density-modified MAD experimental phases contoured at 1.2 and displayed with the refined 6 helix of the DH domain of ITSN. b, Stereo view of a representative portion of the 2F[o]-F[c] electron density of the Dbs -RhoA structure, contoured at 1.3 and displayed with residues 759 -772 of Dbs (yellow) and residues 54 -62 of RhoA (green). c, Ribbon diagram of the ITSN -Cdc42 structure. The DH domain is yellow, and the PH domain is blue, with defined secondary structural elements labeled in accordance with described nomenclature^8. Cdc42 is green, except for the switch regions (s1 = residues 26 -40 and s2 = residues 57 -76), which are red. d, Ribbon diagram of the Dbs -RhoA complex. Coloring and labeling are equivalent to the ITSN -Cdc42 structure. All figures were prepared using SPOCK (http://quorum.tamu.edu/jon/spock/) or MOLSCRIPT36.

Figure 5.
Figure 5. Comparison of the Dbs -RhoA, Dbs -Cdc42 and Tiam1 -Rac1 structures. a, Interface of the DH domain of Dbs (yellow) and Cdc42 (green). b, Interface of the DH domain of Dbs and RhoA (green). c, Superposition of the backbone traces of the 4/ 5 loop of ITSN and Tiam1 on the Dbs -RhoA complex. ITSN (blue) and Tiam1 (red) backbones are semitransparent, and Dbs is yellow. d, Interface of the DH domain of Tiam1 (yellow) and Rac1 (green). Unless otherwise noted, coloring is according to the styles used in Fig. 3.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 468-475) copyright 2002.

Figures were selected by an automated process.