PDBsum entry 1n6h

Protein transport

PDB id: 1n6h

Contents

Protein chain

167 a.a. *

Ligands

GNP

BME

Metals

_MG

Waters ×263

* Residue conservation analysis

PDB id:

1n6h

Name:

Protein transport

Title:

Crystal structure of human rab5a

Structure:

Ras-related protein rab-5a. Chain: a. Fragment: gtpase domain. Synonym: rab5a. Engineered: yes

Source:

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

Resolution:

1.51Å R-factor: 0.177 R-free: 0.190

Authors:

G.Zhu,J.Liu,S.Terzyan,P.Zhai,G.Li,X.C.Zhang

Key ref:

G.Zhu et al. (2003). High resolution crystal structures of human Rab5a and five mutants with substitutions in the catalytically important phosphate-binding loop. J Biol Chem, 278, 2452-2460. PubMed id: 12433916 DOI: 10.1074/jbc.M211042200

Date:

11-Nov-02 Release date: 27-Nov-02

Protein chain

P20339  (RAB5A_HUMAN) -  Ras-related protein Rab-5A from Homo sapiens

Seq: 215 a.a.

Struc: 167 a.a.

Enzyme reactions

• Enzyme class: 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(+)

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

reference

DOI no: 10.1074/jbc.M211042200

J Biol Chem 278:2452-2460 (2003)

PubMed id: 12433916

High resolution crystal structures of human Rab5a and five mutants with substitutions in the catalytically important phosphate-binding loop.

G.Zhu, J.Liu, S.Terzyan, P.Zhai, G.Li, X.C.Zhang.

ABSTRACT

GTPase domain crystal structures of Rab5a wild type and five variants with mutations in the phosphate-binding loop are reported here at resolutions up to 1.5 A. Of particular interest, the A30P mutant was crystallized in complexes with GDP, GDP+AlF(3), and authentic GTP, respectively. The other variant crystals were obtained in complexes with a non-hydrolyzable GTP analog, GppNHp. All structures were solved in the same crystal form, providing an unusual opportunity to compare structures of small GTPases with different catalytic rates. The A30P mutant exhibits dramatically reduced GTPase activity and forms a GTP-bound complex stable enough for crystallographic analysis. Importantly, the A30P structure with bound GDP plus AlF(3) has been solved in the absence of a GTPase-activating protein, and it may resemble that of a transition state intermediate. Conformational changes are observed between the GTP-bound form and the transition state intermediate, mainly in the switch II region containing the catalytic Gln(79) residue and independent of A30P mutation-induced local alterations in the P-loop. The structures suggest an important catalytic role for a P-loop backbone amide group, which is eliminated in the A30P mutant, and support the notion that the transition state of GTPase-mediated GTP hydrolysis is of considerable dissociative character.

Selected figure(s)

Figure 2.
Fig. 2. A30R compared with WT. Crystal structures of A30R ( blue) and WT (red) are superimposed, and their catalytic sites are shown. Also superimposed are the F[obs(A30R)] F[obs(WT]) difference electron densities contoured at 3.5 , with positive density colored in cyan and negative in pink. These densities represent the most significant features in the entire difference map and are typical for all mutants of non-proline substitutions reported here. Mg2+ and ordered water molecules are shown as large and small crosses, respectively.

Figure 3.
Fig. 3. Structures of A30P mutant. A, reduce structural comparison between GppNHp·WT and GTP·A30P. WT is shown in red and A30P in blue. The water hydrogen-bond network around the active site and Mg2+ coordination are shown in dashed lines. Mg2+ and ordered water molecules are shown as large and small crosses, respectively. B, structural comparison among the three A30P complexes. The active sites of GTP- (blue), (GDP+AlF[3])- (red), and GDP- (yellow) forms of A30P are superimposed on each other. C, active site structure of the (GDP+AlF[3])·A30P complex. 2F[obs] F[calc] map was contoured at 1.0 and superimposed with a ball-and-stick model of the final refined structure. Carbon (yellow), nitrogen (blue), oxygen (red), phosphate (white), aluminum (cyan), fluoride (magenta), and magnesium (green) ions are colored, respectively. The coordination of both Mg2+ and Al3+ (except the Al-F bonds) are shown in thin lines. Orientations are the same as that of Fig. 2.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 2452-2460) copyright 2003.

Figures were selected by an automated process.