PDBsum entry 2zzv

Transport protein

PDB id: 2zzv

Contents

Protein chains

330 a.a. *

Ligands

LAC ×2

Metals

_CA ×2

Waters ×940

* Residue conservation analysis

PDB id:

2zzv

Name:

Transport protein

Title:

Crystal structure of a periplasmic substrate binding protein in complex with calcium and lactate

Structure:

Abc transporter, solute-binding protein. Chain: a, b. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 300852. Gene: ttha0766. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.40Å R-factor: 0.165 R-free: 0.185

Authors:

N.Akiyama,K.Takeda,K.Miki

Key ref:

N.Akiyama et al. (2009). Crystal structure of a periplasmic substrate-binding protein in complex with calcium lactate. J Mol Biol, 392, 559-565. PubMed id: 19631222 DOI: 10.1016/j.jmb.2009.07.043

Date:

27-Feb-09 Release date: 11-Aug-09

Protein chains

Q5SK82  (TLBP_THET8) -  Lactate-binding periplasmic protein TTHA0766 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 361 a.a.

Struc: 330 a.a.

DOI no: 10.1016/j.jmb.2009.07.043

J Mol Biol 392:559-565 (2009)

PubMed id: 19631222

Crystal structure of a periplasmic substrate-binding protein in complex with calcium lactate.

N.Akiyama, K.Takeda, K.Miki.

ABSTRACT

Lactate is utilized in many biological processes, and its transport across biological membranes is mediated with various types of transporters. Here, we report the crystal structures of a lactate-binding protein of a TRAP (tripartite ATP-independent periplasmic) secondary transporter from Thermus thermophilus HB8. The folding of the protein is typical for a type II periplasmic solute-binding protein and forms a dimer in a back-to-back manner. One molecule of l-lactate is clearly identified in a cleft of the protein as a complex with a calcium ion. Detailed crystallographic and biochemical analyses revealed that the calcium ion can be removed from the protein and replaced with other divalent cations. This characterization of the structure of a protein binding with calcium lactate makes a significant contribution to our understanding of the mechanisms by which calcium and lactate are accommodated in cells.

Selected figure(s)

Figure 2.
Fig. 2. Crystal structure of TTHA0766 from T. thermophilus HB8. (a) The monomer structure is represented as a ribbon model, in which domains I and II are shown in green and magenta, respectively. The additional C-terminal helices are shown in yellow. Liganded calcium ion and lactate molecule are shown as CPK and stick models, respectively. (b) Side view of (a) rotated by 90° around the vertical axis. (c) The dimer structure is represented as a tube model. Chain A, cyan; chain B, gray. (d) Interprotomer interactions. The side chains involved in the interactions are shown as sticks. Asterisks denote residues of another subunit. Salt bridges are indicated as orange dashed lines.

Figure 4.
Fig. 4. Structural features of the form II and III crystals. (a) The anomalous difference Fourier maps of form II are shown at the 3σ and 6σ levels as red and blue meshes, respectively. Maps were calculated using the refined phases of form II (Table 1) and the amplitude of structure factors from the data sets collected at low-remote (λ = 1.2896 Å), peak (λ = 1.2810 Å) and high-remote wavelengths (λ = 1.2569 Å) of zinc (Table S1). (b) The binding site of form II. (c) The binding site of form III. The structure of form I is superimposed as a semitransparent model in gray for comparison of (b) and (c).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 392, 559-565) copyright 2009.

Figures were selected by an automated process.