PDBsum entry 1vgl

Circadian clock protein

PDB id: 1vgl

Contents

Protein chains

96 a.a. *

105 a.a. *

Metals

_HG ×2

Waters ×93

* Residue conservation analysis

PDB id:

1vgl

Name:

Circadian clock protein

Title:

Crystal structure of tetrameric kaib from t.Elongatus bp-1

Structure:

Circadian clock protein kaib. Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

Thermosynechococcus elongatus bp-1. Organism_taxid: 197221. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.60Å R-factor: 0.230 R-free: 0.289

Authors:

R.Iwase,K.Imada,F.Hayashi,T.Uzumaki,K.Namba,M.Ishiura

Key ref:

R.Iwase et al. (2005). Functionally important substructures of circadian clock protein KaiB in a unique tetramer complex. J Biol Chem, 280, 43141-43149. PubMed id: 16227211 DOI: 10.1074/jbc.M503360200

Date:

27-Apr-04 Release date: 16-Aug-05

Protein chains

Q79V61  (KAIB_THEEB) -  Circadian clock oscillator protein KaiB from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 108 a.a.

Struc: 96 a.a.*

Protein chains

Q79V61  (KAIB_THEEB) -  Circadian clock oscillator protein KaiB from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 108 a.a.

Struc: 105 a.a.*

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

DOI no: 10.1074/jbc.M503360200

J Biol Chem 280:43141-43149 (2005)

PubMed id: 16227211

Functionally important substructures of circadian clock protein KaiB in a unique tetramer complex.

R.Iwase, K.Imada, F.Hayashi, T.Uzumaki, M.Morishita, K.Onai, Y.Furukawa, K.Namba, M.Ishiura.

ABSTRACT

KaiB is a component of the circadian clock molecular machinery in cyanobacteria, which are the simplest organisms that exhibit circadian rhythms. Here we report the x-ray crystal structure of KaiB from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. The KaiB crystal diffracts at a resolution of 2.6 A and includes four subunits organized as a dimer of dimers, each composed of two non-equivalent subunits. The overall shape of the tetramer is an elongated hexagonal plate, with a single positively charged cleft flanked by two negatively charged ridges whose surfaces includes several terminal chains. Site-directed mutagenesis of Synechococcus KaiB confirmed that alanine substitution of residues Lys-11 or Lys-43 in the cleft, or deletion of C-terminal residues 95-108, which forms part of the ridges, strongly weakens in vivo circadian rhythms. Characteristics of KaiB deduced from the x-ray crystal structure were also confirmed by physicochemical measurements of KaiB in solution. These data suggest that the positively charged cleft and flanking negatively charged ridges in KaiB are essential for the biological function of KaiB in the circadian molecular machinery in cyanobacteria.

Selected figure(s)

Figure 2.
FIGURE 2. X-ray crystal structure of KaiB tetramer. A, crystal packing of KaiB represented as a C backbone diagram. Each asymmetric unit of the crystal of the mutant KaiB T64C contained two independent dimers (AB and CD). Each dimer formed a tetramer (T1 and T2) with a crystallographic 2-fold axis (black oval). Molecules related by crystallographic 2-fold axes are indicated by the same color. Other tetramers (pale gray) were also generated by the crystallographic symmetry. The black frame indicates a unit cell. B, structure of KaiB monomer represented as a ribbon diagram. Helices and strands are shown in orange and green, respectively. C, comparison of the structures of four independent KaiB subunits in the asymmetric unit. C traces of all four subunits are superimposed in stereo diagram. Subunits A, B, C, and D are shown in green, orange, cyan, and blue, respectively. The figures were generated with MOLSCRIPT (28) and Raster3D (29).

Figure 6.
FIGURE 6. Electrostatic surface potential of the KaiB tetramer. A, stereo view of C backbone ribbon diagram, color-coded according to the amino acid sequence in rainbow color from the N terminus in blue to the C terminus in red. Side chains of residues for which substitution mutations were examined (Fig. 7) are displayed in ball and stick representation. The figure was generated with MOLSCRIPT (28) and Raster3D (29). B, electrostatic potential of surface SBB'T. The saturation threshold for the Grasp image is -10 and +10. C, electrostatic potential of surface SAA'T. D, electrostatic potential of surface SBB'T after C-terminal 14 residues are truncated (KaiB[1–94]). Electrostatic surface potential is color-coded: blue, positive; red, negative. The figures are made by using GRASP (30) and Raster3D (29). The negative ridges are outlined with dotted lines. The positive cleft and positive hollows are indicated by yellow and black arrowheads, respectively. The acidic and basic residues in the positive cleft, negative ridges, and positive hollow are labeled.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 43141-43149) copyright 2005.

Figures were selected by the author.