PDBsum entry 1i4d

Signaling protein

PDB id: 1i4d

Contents

Protein chains

188 a.a. *

177 a.a. *

Ligands

GDP

Metals

_MG

Waters ×147

* Residue conservation analysis

PDB id:

1i4d

Name:

Signaling protein

Title:

Crystal structure analysis of rac1-gdp complexed with arfaptin (p21)

Structure:

Arfaptin 2. Chain: a, b. Fragment: residues 118-341. Synonym: partner of rac1. Engineered: yes. Ras-related c3 botulinum toxin substrate 1. Chain: d. Synonym: p21-rac1. Engineered: yes

Source:

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

Biol. unit:

Trimer (from PQS)

Resolution:

2.50Å R-factor: 0.238 R-free: 0.298

Authors:

C.Tarricone,B.Xiao,N.Justin,S.J.Gamblin,S.J.Smerdon

Key ref:

C.Tarricone et al. (2001). The structural basis of Arfaptin-mediated cross-talk between Rac and Arf signalling pathways. Nature, 411, 215-219. PubMed id: 11346801 DOI: 10.1038/35075620

Date:

20-Feb-01 Release date: 16-May-01

Protein chains

P53365  (ARFP2_HUMAN) -  Arfaptin-2 from Homo sapiens

Seq: 341 a.a.

Struc: 188 a.a.

Protein chain

P63000  (RAC1_HUMAN) -  Ras-related C3 botulinum toxin substrate 1 from Homo sapiens

Seq: 192 a.a.

Struc: 177 a.a.

Enzyme reactions

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

GTP + H2O = GDP (Bound ligand (Het Group name = GDP) corresponds exactly) + 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: 10.1038/35075620

Nature 411:215-219 (2001)

PubMed id: 11346801

The structural basis of Arfaptin-mediated cross-talk between Rac and Arf signalling pathways.

C.Tarricone, B.Xiao, N.Justin, P.A.Walker, K.Rittinger, S.J.Gamblin, S.J.Smerdon.

ABSTRACT

Small G proteins are GTP-dependent molecular switches that regulate numerous cellular functions. They can be classified into homologous subfamilies that are broadly associated with specific biological processes. Cross-talk between small G-protein families has an important role in signalling, but the mechanism by which it occurs is poorly understood. The coordinated action of Arf and Rho family GTPases is required to regulate many cellular processes including lipid signalling, cell motility and Golgi function. Arfaptin is a ubiquitously expressed protein implicated in mediating cross-talk between Rac (a member of the Rho family) and Arf small GTPases. Here we show that Arfaptin binds specifically to GTP-bound Arf1 and Arf6, but binds to Rac.GTP and Rac.GDP with similar affinities. The X-ray structure of Arfaptin reveals an elongated, crescent-shaped dimer of three-helix coiled-coils. Structures of Arfaptin with Rac bound to either GDP or the slowly hydrolysable analogue GMPPNP show that the switch regions adopt similar conformations in both complexes. Our data highlight fundamental differences between the molecular mechanisms of Rho and Ras family signalling, and suggest a model of Arfaptin-mediated synergy between the Arf and Rho family signalling pathways.

Selected figure(s)

Figure 1.
Figure 1: Sequence homology and structure of Arfaptin. a, Sequence homology between five Arfaptin homologues. The -helical elements derived from the crystal structure are indicated and coloured as in b. The N terminus of the Arfaptin fragment used in this study, which encompasses the entire predicted coiled-coil region of these molecules, is indicated by the black triangle. Residues absolutely conserved between the six Arfaptin homologues are indicated by blue circles. b, Three orthogonal views of the Arfaptin dimer in ribbons representation26. Top, Arfaptin dimer viewed along its dyad axis. Helices A, B and C of each monomer are red, green and blue, respectively, and the dimer-related helices are labelled A', B' and C'. Middle, Arfaptin dimer viewed along the long axis, illustrating the cavity created by the five-helix barrel at the dimer interface. Bottom, Arfaptin viewed with its long axis horizontal and the dyad axis vertical, showing the crescent-like shape of the dimer.

Figure 3.
Figure 3: Structure of the Rac -Arfaptin complex. a, Rac -Arfaptin complex shown in ribbons representation, with Arfaptin in the same orientation as shown in Fig. 1b, bottom. Helices of the Rac are red, -strands are green and the nucleotide is in yellow ball-and-stick representation. One monomer of the Arfaptin dimer is shown in blue, the other in pink. b, Arfaptin -Rac interface shown as an 'open book' representation. The C positions of residues that interact are indicated by white spheres. Residue type and number are shown in black type with interacting residues from the other protein indicated in red (hydrogen-bonding interactions) or green (non-polar/van der Waals interactions). Asterisk denotes His 57 from Arfaptin molecule 'B' of the dimer (blue); all other Arfaptin residues are contributed from molecule 'A' (yellow). The two 'switch' regions of Rac are highlighted in red.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2001, 411, 215-219) copyright 2001.

Figures were selected by the author.