PDBsum entry: 3cb2

Structural protein, hydrolase

PDB id: 3cb2

Contents

Protein chains

432 a.a. *

Ligands

GDP ×2

Waters ×378

* Residue conservation analysis

PDB id:

3cb2

Name:

Structural protein, hydrolase

Title:

Crystal structure of human gamma-tubulin bound to gdp

Structure:

Tubulin gamma-1 chain. Chain: a, b. Synonym: gamma-1-tubulin. Gamma-tubulin complex component 1. Gcp-1. Engineered: yes

Source:

Homo sapiens. Human. Gene: tubg1, tubg. Expressed in: spodoptera frugiperda.

Resolution:

2.30Å R-factor: 0.189 R-free: 0.238

Authors:

L.M.Rice,E.A.Montabana,D.A.Agard

Key ref:

L.M.Rice et al. (2008). The lattice as allosteric effector: structural studies of alphabeta- and gamma-tubulin clarify the role of GTP in microtubule assembly. Proc Natl Acad Sci U S A, 105, 5378-5383. PubMed id: 18388201 DOI: 10.1073/pnas.0801155105

Date:

21-Feb-08 Release date: 10-Jun-08

Protein chains

P23258  (TBG1_HUMAN) -  Tubulin gamma-1 chain

Seq: 451 a.a.

Struc: 432 a.a.*

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

 Gene Ontology (GO) functional annotation 

• Cellular component: protein complex (16 terms)
• Biological process: microtubule-based process (7 terms)
• Biochemical function: nucleotide binding (5 terms)

DOI no: 10.1073/pnas.0801155105

Proc Natl Acad Sci U S A 105:5378-5383 (2008)

PubMed id: 18388201

The lattice as allosteric effector: structural studies of alphabeta- and gamma-tubulin clarify the role of GTP in microtubule assembly.

L.M.Rice, E.A.Montabana, D.A.Agard.

ABSTRACT

GTP-dependent microtubule polymerization dynamics are required for cell division and are accompanied by domain rearrangements in the polymerizing subunit, alphabeta-tubulin. Two opposing models describe the role of GTP and its relationship to conformational change in alphabeta-tubulin. The allosteric model posits that unpolymerized alphabeta-tubulin adopts a more polymerization-competent conformation upon GTP binding. The lattice model posits that conformational changes occur only upon recruitment into the growing lattice. Published data support a lattice model, but are largely indirect and so the allosteric model has prevailed. We present two independent solution probes of the conformation of alphabeta-tubulin, the 2.3 A crystal structure of gamma-tubulin bound to GDP, and kinetic simulations to interpret the functional consequences of the structural data. These results (with our previous gamma-tubulin:GTPgammaS structure) support the lattice model by demonstrating that major domain rearrangements do not occur in eukaryotic tubulins in response to GTP binding, and that the unpolymerized conformation of alphabeta-tubulin differs significantly from the polymerized one. Thus, geometric constraints of lateral self-assembly must drive alphabeta-tubulin conformational changes, whereas GTP plays a secondary role to tune the strength of longitudinal contacts within the microtubule lattice. alphabeta-Tubulin behaves like a bent spring, resisting straightening until forced to do so by GTP-mediated interactions with the growing microtubule. Kinetic simulations demonstrate that resistance to straightening opposes microtubule initiation by specifically destabilizing early assembly intermediates that are especially sensitive to the strength of lateral interactions. These data provide new insights into the molecular origins of dynamic microtubule behavior.

Selected figure(s)

Figure 1.
Two conformations of αβ-tubulin, and conflicting models for the role of GTP. (a) Longitudinal and lateral interaction surfaces are aligned in the straight (1JFF, top), but not in the curved (1SA0, bottom) conformation. In the curved conformation, the α- and β-tubulin protofilament and lateral interaction axes are skewed by 11° and 6°, respectively; these rearrangements separate equivalent laterally interacting atoms by up to 6 Å. (Inset) This misalignment of interfaces destabilizes lateral interactions between curved αβ-tubulins. (b) In the allosteric model, GTP (circled in red) stimulates MT assembly by inducing the straight, MT-compatible conformation in unpolymerized αβ-tubulin. Incorporation into the lattice is not associated with unfavorable domain rearrangements (ΔG [straight] = 0). (c) In the lattice model, unpolymerized αβ-tubulin remains curved even when bound to GTP. Incorporation into the lattice requires unfavorable domain rearrangements (ΔG [straight] = E). The lattice-acting GTP (circled in red) provides stronger lattice contacts to stabilize the MT-bound straight conformation.

Figure 2.
Structural features of γ-tubulin:GDP. (a) F [o] − F [c] electron density computed from the final model with GDP omitted. The nucleotide binding site of chain A is shown. (b) The twofold noncrystallographic symmetry interaction between γ-tubulins (Chain A, dark blue and yellow; Chain B, light blue and pale yellow). The nucleotide binding sites (“plus” ends) are top and bottom. (c) γ-Tubulin:GDP (chain A, dark blue; chain B, light blue) and γ-tubulin:GTPγS (tan) adopt the same curved domain organization. See also Table S2. (Left) Helices H6 and H7. (Right) The intermediate domain β-sheet (helix H10, which would obscure the view of the β-sheet, has been omitted for clarity). (d) γ-tubulin:GDP (colors as in c) shows characteristic differences when compared with the straight conformation of β-tubulin (PDB code: 1JFF, orange). Left and Right are as in c.

Figures were selected by an automated process.