PDBsum entry 2ffq

Hydrolase

PDB id: 2ffq

Contents

Protein chain

164 a.a. *

Ligands

GSP

Metals

_MG

Waters ×132

* Residue conservation analysis

PDB id:

2ffq

Name:

Hydrolase

Title:

The crystal structure of human neuronal rab6b in its active gtpgs- bound form

Structure:

Ras-related protein rab-6b. Chain: a. Synonym: rab6b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: rab6b. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.78Å R-factor: 0.191 R-free: 0.202

Authors:

I.Garcia-Saez,S.Tcherniuk,F.Kozielski

Key ref:

I.Garcia-Saez et al. (2006). The structure of human neuronal Rab6B in the active and inactive form. Acta Crystallogr D Biol Crystallogr, 62, 725-733. PubMed id: 16790928 DOI: 10.1107/S0907444906015319

Date:

20-Dec-05 Release date: 04-Jul-06

Protein chain

Q9NRW1  (RAB6B_HUMAN) -  Ras-related protein Rab-6B from Homo sapiens

Seq: 208 a.a.

Struc: 164 a.a.*

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

Enzyme reactions

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

GTP (Bound ligand (Het Group name = GSP) matches with 93.94% similarity) + H2O = GDP + phosphate + H(+)

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

reference

DOI no: 10.1107/S0907444906015319

Acta Crystallogr D Biol Crystallogr 62:725-733 (2006)

PubMed id: 16790928

The structure of human neuronal Rab6B in the active and inactive form.

I.Garcia-Saez, S.Tcherniuk, F.Kozielski.

ABSTRACT

The Rab small G-protein family plays important roles in eukaryotes as regulators of vesicle traffic. In Rab proteins, the hydrolysis of GTP to GDP is coupled with association with and dissociation from membranes. Conformational changes related to their different nucleotide states determine their effector specificity. The crystal structure of human neuronal Rab6B was solved in its 'inactive' (with bound MgGDP) and 'active' (MgGTPgammaS-bound) forms to 2.3 and 1.8 A, respectively. Both crystallized in space group P2(1)2(1)2(1), with similar unit-cell parameters, allowing the comparison of both structures without packing artifacts. Conformational changes between the inactive GDP and active GTP-like state are observed mainly in the switch I and switch II regions, confirming their role as a molecular switch. Compared with other Rab proteins, additional changes are observed in the Rab6 subfamily-specific RabSF3 region that might contribute to the specificity of Rab6 for its different effector proteins.

Selected figure(s)

Figure 3.
Figure 3 (a) Assignment of secondary-structural elements of Rab6B-GTP S (grey) and Rab6B-GDP (blue). The areas of high flexibility (higher B factor) found in the Rab6B-GDP structure are highlighted in red (a star indicates the area of disorder around switch I and a circle indicates the area of disorder around switch II) and green (inside SF3 region). (b) Structural alignment of Rab6B-GTP S and Rab6B-GDP following the same colour code.

Figure 5.
Figure 5 Surface representation of Rab6B-GDP (a, c) and Rab6B-GTP S (b, d). The surface corresponding to the switch I and switch II regions is coloured in red. The neighbouring modified areas are depicted in green and include helix 3, the N-terminal area of 5, which forms the SF3 consensus domain, 1 ( 2 in Rab6B-GDP) and guanine nucleotide-binding G2. (c) and (d) are views of (a) and (b) from below, respectively. The locations of the three residues that differ with respect to Rab6A' are highlighted in yellow; an asterisk indicates that the residue is buried.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 725-733) copyright 2006.

Figures were selected by an automated process.