1N6K

Crystal Structure of Human Rab5a A30P mutant complex with GDP and aluminum fluoride

Summary for 1N6K

• Entry DOI: 10.2210/pdb1n6k/pdb
• Related: 1N6H 1N6I 1N6L 1N6N 1N6O 1N6P 1N6R
• Descriptor: Ras-related protein Rab-5A, MAGNESIUM ION, GUANOSINE-5'-DIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: rab, gtpase, protein transport
• Biological source: Homo sapiens (human)
• Cellular location: Cell membrane; Lipid-anchor; Cytoplasmic side (By similarity): P20339
• Total number of polymer chains: 1
• Total formula weight: 19643.23

Authors

Zhu, G.,Liu, J.,Terzyan, S.,Zhai, P.,Li, G.,Zhang, X.C. (deposition date: 2002-11-11, release date: 2002-11-27, Last modification date: 2021-10-27)

Primary citation

Zhu, G.,Liu, J.,Terzyan, S.,Zhai, P.,Li, G.,Zhang, X.C.
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, 2003

PubMed 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.

PubMed: 12433916
DOI: 10.1074/jbc.M211042200

Experimental method

X-RAY DIFFRACTION (1.55 Å)