PDBsum entry 3n5c

Protein transport

PDB id: 3n5c

Contents

Protein chains

147 a.a. *

160 a.a. *

Ligands

GDP ×2

Metals

_CL ×3

Waters ×172

* Residue conservation analysis

PDB id:

3n5c

Name:

Protein transport

Title:

Crystal structure of arf6delta13 complexed with gdp

Structure:

Adp-ribosylation factor 6. Chain: a, b. Fragment: unp residues 14-175. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: arf6. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.82Å R-factor: 0.172 R-free: 0.195

Authors:

K.Aizel,V.Biou,J.Cherfils

Key ref:

V.Biou et al. (2010). SAXS and X-ray crystallography suggest an unfolding model for the GDP/GTP conformational switch of the small GTPase Arf6. J Mol Biol, 402, 696-707. PubMed id: 20709080

Date:

25-May-10 Release date: 18-Aug-10

Protein chain

P62330  (ARF6_HUMAN) -  ADP-ribosylation factor 6 from Homo sapiens

Seq: 175 a.a.

Struc: 147 a.a.

Protein chain

P62330  (ARF6_HUMAN) -  ADP-ribosylation factor 6 from Homo sapiens

Seq: 175 a.a.

Struc: 160 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: 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(+)

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

reference

J Mol Biol 402:696-707 (2010)

PubMed id: 20709080

SAXS and X-ray crystallography suggest an unfolding model for the GDP/GTP conformational switch of the small GTPase Arf6.

V.Biou, K.Aizel, P.Roblin, A.Thureau, E.Jacquet, S.Hansson, B.Guibert, E.Guittet, C.van Heijenoort, M.Zeghouf, J.Perez, J.Cherfils.

ABSTRACT

The small GTPases Arf1 and Arf6 have nonoverlapping functions in cellular traffic despite their very high sequence and structural resemblance. Notably, the exquisite isoform specificity of their guanine nucleotide exchange factors and their distinctive sensitivity to the drug brefeldin A cannot be explained by any straightforward structural model. Here we integrated structural and spectroscopic methods to address this issue using Δ13Arf6-GDP, a truncated mutant that mimics membrane-bound Arf6-GDP. The crystal structure of Δ13Arf6-GDP reveals an unprecedented unfolding of the GTPase core β-strands, which is fully accounted for by small-angle X-ray scattering data in solution and by ab initio three-dimensional envelope calculation. NMR chemical shifts identify this structural disorder in Δ13Arf6-GDP, but not in the closely related Δ17Arf1-GDP, which is consistent with their comparative thermodynamic and hydrodynamic analyses. Taken together, these experiments suggest an unfolding model for the nucleotide switch of Arf6 and shed new light on its biochemical differences with Arf1.