PDBsum entry 2bto

Cytoskeletal protein

PDB id: 2bto

Contents

Protein chains

413 a.a. *

423 a.a. *

103 a.a. *

Ligands

GTP ×2

Waters ×216

* Residue conservation analysis

PDB id:

2bto

Name:

Cytoskeletal protein

Title:

Structure of btuba from prosthecobacter dejongeii

Structure:

Tubulin btuba. Chain: a, b. Engineered: yes. Thioredoxin 1. Chain: t. Synonym: trx1, trx. Engineered: yes

Source:

Prosthecobacter dejongeii. Organism_taxid: 48465. Atcc: 27091. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: german collection of microorganisms (dsm 12251). Escherichia coli. Organism_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Nonamer (from PDB file)

Resolution:

2.50Å R-factor: 0.202 R-free: 0.235

Authors:

D.Schlieper,J.Lowe

Key ref:

D.Schlieper et al. (2005). Structure of bacterial tubulin BtubA/B: evidence for horizontal gene transfer. Proc Natl Acad Sci U S A, 102, 9170-9175. PubMed id: 15967998 DOI: 10.1073/pnas.0502859102

Date:

04-Jun-05 Release date: 23-Jun-05

Protein chain

Q8GCC5  (Q8GCC5_9BACT) -  Tubulin from Prosthecobacter dejongeii

Seq: 473 a.a.

Struc: 413 a.a.*

Protein chain

Q8GCC5  (Q8GCC5_9BACT) -  Tubulin from Prosthecobacter dejongeii

Seq: 473 a.a.

Struc: 423 a.a.*

Protein chain

P0AA25  (THIO_ECOLI) -  Thioredoxin 1 from Escherichia coli (strain K12)

Seq: 109 a.a.

Struc: 103 a.a.

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

DOI no: 10.1073/pnas.0502859102

Proc Natl Acad Sci U S A 102:9170-9175 (2005)

PubMed id: 15967998

Structure of bacterial tubulin BtubA/B: evidence for horizontal gene transfer.

D.Schlieper, M.A.Oliva, J.M.Andreu, J.Löwe.

ABSTRACT

alphabeta-Tubulin heterodimers, from which the microtubules of the cytoskeleton are built, have a complex chaperone-dependent folding pathway. They are thought to be unique to eukaryotes, whereas the homologue FtsZ can be found in bacteria. The exceptions are BtubA and BtubB from Prosthecobacter, which have higher sequence homology to eukaryotic tubulin than to FtsZ. Here we show that some of their properties are different from tubulin, such as weak dimerization and chaperone-independent folding. However, their structure is strikingly similar to tubulin including surface loops, and BtubA/B form tubulin-like protofilaments. Presumably, BtubA/B were transferred from a eukaryotic cell by horizontal gene transfer because their high degree of similarity to eukaryotic genes is unique within the Prosthecobacter genome.

Selected figure(s)

Figure 2.
Fig. 2. BtubA/B polymers have a longitudinal repeat similar to , -tubulin indicating protofilament formation. (A) Low-magnification micrograph showing BtubA/B filaments after polymerization in the presence of GTP. Protein at 10 µM was incubated for 30 min at ambient temperature with 100 mM Pipes·NaOH (pH 6.8), 5 mM MgCl[2], 200 mM KCl, and 1 mM GTP and was negatively stained with 2% uranyl acetate. (B-D) BtubA/B double filaments. These are the most commonly formed filaments, presumably consisting of two BtubA/B protofilaments. Most filaments twist (B and C), indicated by arrowheads at the crossover points. Filament C has an average width of 109 Å. (Scale bar: 100 nM.) (E) Computed diffraction pattern of filament B. Layer lines are clearly visible at 42 Å, representing the subunit repeat along the protofilament axis. This repeat matches the repeat seen in the BtubA/B crystal structure and is close to that of tubulin (40 Å).

Figure 3.
Fig. 3. Crystal structures of BtubA and BtubA/B. (A) Crystal structure of BtubA at 2.5-Å resolution. BtubA's structure is closely related to tubulin. The fold is divided into the N-terminal nucleotide-binding domain (blue), separated by helix H7 (yellow) from the intermediate domain (orange) and two large helices forming the C-terminal domain (red) (4). (B) BtubA contains the C-terminal tubulin domain. Shown is a view rotated 90° around the y axis from A. The two large helices (red) at the C terminus of tubulin form the outside of microtubules (7) and make the biggest difference between tubulin and FtsZ. (C) Crystal structure of BtubA/B heterodimer (asymmetric unit of the crystals) at 3.2-Å resolution. BtubA/B form the same heterodimer as tubulin (24, 25). The protofilament axis is vertical. BtubA is situated at the plus (+) end (red), and BtubB is at the minus (-) end (blue). In the crystals, BtubA contains GDP, whereas BtubB has a sulfate ion in the nucleotide-binding site. The heterodimer is not completely straight; the two subunits are rotated by 15° around the z axis [same direction as in the tubulin-stathmin complex (26)], tangential to the microtubule wall. (D) The BtubA/B crystals contain a continuous double filament. The 6[5]22 space group symmetry produces an antiparallel double filament with repeating BtubA/B units in the crystal packing. The bend per heterodimer is 60°, divided into 15° between BtubA and -B (intradimer; see C) and 45° between B and A (interdimer). (E) BtubA/B are very closely related to tubulin. Shown is the superposition of BtubA (black) (rmsd to BtubB, 1.34 Å; 36% sequence identity; 82% aligned) with -tubulin (25) (green; rmsd 1.5 Å; 37% sequence identity; 85% aligned; Protein Data Bank ID code 1JFF [PDB] ), -tubulin (25) (red; rmsd 1.71 Å; 35% sequence identity; 85% aligned; Protein Data Bank ID code 1JFF [PDB] ), and subunit B from the tubulin-stathmin complex (26) (blue; rmsd 1.3 Å; 35% sequence identity; 85% aligned; Protein Data Bank ID code 1SA0 [PDB] ). Differences are small and mainly located in the T7-loop, the M-loop, which is involved in microtubule formation for tubulin (7), helix H6, and loop H1-S2, which are part of the protofilament contact. BtubA/B have a short S9-S10 loop that in -tubulin covers the Taxol-binding pocket completely. (Figure was generated with PYMOL.

Figures were selected by an automated process.