PDBsum entry 2ot3

Protein transport

PDB id: 2ot3

Contents

Protein chains

253 a.a. *

157 a.a. *

Waters ×463

* Residue conservation analysis

PDB id:

2ot3

Name:

Protein transport

Title:

Crystal structure of rabex-5 vps9 domain in complex with nucleotide free rab21

Structure:

Rab5 gdp/gtp exchange factor. Chain: a. Fragment: residues 132-297. Synonym: rabex-5, rabaptin-5-associated exchange factor for rab5, rap1. Engineered: yes. Ras-related protein rab-21. Chain: b. Fragment: residues 16-183.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: rabgef1, rabex5. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: rab21, kiaa0118.

Resolution:

2.10Å R-factor: 0.191 R-free: 0.243

Authors:

A.Delprato,D.Lambright

Key ref:

A.Delprato and D.G.Lambright (2007). Structural basis for Rab GTPase activation by VPS9 domain exchange factors. Nat Struct Mol Biol, 14, 406-412. PubMed id: 17450153 DOI: 10.1038/nsmb1232

Date:

07-Feb-07 Release date: 24-Apr-07

Protein chain

Q9UJ41  (RABX5_HUMAN) -  Rab5 GDP/GTP exchange factor from Homo sapiens

Seq: 491 a.a.

Struc: 253 a.a.

Protein chain

Q9UL25  (RAB21_HUMAN) -  Ras-related protein Rab-21 from Homo sapiens

Seq: 225 a.a.

Struc: 157 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.?

DOI no: 10.1038/nsmb1232

Nat Struct Mol Biol 14:406-412 (2007)

PubMed id: 17450153

Structural basis for Rab GTPase activation by VPS9 domain exchange factors.

A.Delprato, D.G.Lambright.

ABSTRACT

RABEX-5 and other exchange factors with VPS9 domains regulate endocytic trafficking through activation of the Rab family GTPases RAB5, RAB21 and RAB22. Here we report the crystal structure of the RABEX-5 catalytic core in complex with nucleotide-free RAB21, a key intermediate in the exchange reaction pathway. The structure reveals how VPS9 domain exchange factors recognize Rab GTPase substrates, accelerate GDP release and stabilize the nucleotide-free conformation. We further identify an autoinhibitory element in a predicted amphipathic helix located near the C terminus of the VPS9 domain. The autoinhibitory element overlaps with the binding site for the multivalent effector RABAPTIN-5 and potently suppresses the exchange activity of RABEX-5. Autoinhibition can be partially reversed by mutation of conserved residues on the nonpolar face of the predicted amphipathic helix or by assembly of the complex with RABAPTIN-5.

Selected figure(s)

Figure 1.
Figure 1. Structure of the RABEX-5 HB-VPS9 tandem in complex with nucleotide-free RAB21. (a) Ribbon representation. The catalytic core of RABEX-5 consists of a helical bundle (light brown; HB1– HB4), a VPS9 domain (brown; V1– V6) and a C-terminal helix (dark brown; C). RAB21 ( 1– 5 and 1– 6) is depicted in gray with the P-loop, switch and interswitch regions colored as indicated. (b) Docking of nonpolar residues in the switch and interswitch regions of Rab21 in the hydrophobic groove between the V4 and V6 helices of the VPS9 domain. RABEX-5 is depicted as a gray ribbon with yellow side chains underneath a semitransparent surface. RAB21 is depicted as a tube with side chains. (c) Network of intermolecular polar interactions at the RAB21–VPS9 domain interface. Dotted lines represent hydrogen bonds.

Figure 3.
Figure 3. Comparison with the nucleotide-free Sec7–Arf GTPase complex. (a) Nucleotide-free RAB21 in complex with the HB-VPS9 tandem of RABEX-5. (b) Nucleotide-free ARF1 in complex with the Sec7 domain of Gea2 (ref. 39). The helices that comprise the core of the GTPase-binding sites in the VPS9 and Sec7 domains are depicted in brown. The invariant P-loop lysine (RAB21 and ARF1), aspartic acid finger (VPS9 domain) and glutamic acid finger (Sec7 domain) are depicted as spheres.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2007, 14, 406-412) copyright 2007.

Figures were selected by an automated process.