PDBsum entry 1m2f

Circadian clock protein

PDB id: 1m2f

Contents

Protein chain

135 a.a. *

* Residue conservation analysis

PDB id:

1m2f

Name:

Circadian clock protein

Title:

Solution structure of the n-terminal domain of synechococcus elongatus kaia (kaia135n); family of 25 structures

Structure:

Kaia. Chain: a. Fragment: n-terminal domain (residues 1-135). Engineered: yes

Source:

Synechococcus elongatus. Organism_taxid: 32046. Gene: kaia. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

25 models

Authors:

S.B.Williams,I.Vakonakis,S.S.Golden,A.C.Liwang

Key ref:

S.B.Williams et al. (2002). Structure and function from the circadian clock protein KaiA of Synechococcus elongatus: a potential clock input mechanism. Proc Natl Acad Sci U S A, 99, 15357-15362. PubMed id: 12438647 DOI: 10.1073/pnas.232517099

Date:

23-Jun-02 Release date: 13-Nov-02

Protein chain

Q79PF6  (KAIA_SYNE7) -  Circadian clock oscillator protein KaiA from Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)

Seq: 284 a.a.

Struc: 135 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1073/pnas.232517099

Proc Natl Acad Sci U S A 99:15357-15362 (2002)

PubMed id: 12438647

Structure and function from the circadian clock protein KaiA of Synechococcus elongatus: a potential clock input mechanism.

S.B.Williams, I.Vakonakis, S.S.Golden, A.C.LiWang.

ABSTRACT

In the cyanobacterium Synechococcus elongatus (PCC 7942) the proteins KaiA, KaiB, and KaiC are required for circadian clock function. We deduced a circadian clock function for KaiA from a combination of biochemical and structural data. Both KaiA and its isolated carboxyl-terminal domain (KaiA180C) stimulated KaiC autophosphorylation and facilitated attenuation of KaiC autophosphorylation by KaiB. An amino-terminal domain (KaiA135N) had no function in the autophosphorylation assay. NMR structure determination showed that KaiA135N is a pseudo-receiver domain. We propose that this pseudo-receiver is a timing input-device that regulates KaiA stimulation of KaiC autophosphorylation, which in turn is essential for circadian timekeeping.

Selected figure(s)

Figure 3.
Fig 3. The solution structure of KaiA135N and comparisons to other receiver domain proteins. -strands are in blue, -helices are in purple, and the flexible loop of KaiA135N and the equivalent region of other receiver domains are in gold. The structure coordinates have been deposited in the Protein Data Bank under PDB ID codes 1M2E and 1M2F for the average minimized structure and the family of structures, respectively. (Ai) Schematic representation of the average minimized structure. The solution structure of KaiA135N is an - - sandwich built around a five-parallel-strand -sheet with b-a-c-d-e arrangement. The rotational correlation time ( [c]) was calculated to be 8.2 ns, which is consistent with a monomer in solution (21). (Aii) Stereoview of the overlaid backbone of a family of 25 low-energy structures calculated from 2,034 distance and geometry restraints. The backbone rms deviation from the average is 0.38 ± 0.04 Å for residues 4-83 and 98-135. The rms deviation for all heavy atoms is 0.78 ± 0.05 Å for the same residues. Few medium- or long-range NOE contacts were identified for residues 83-97, and 15N dynamics (see supporting information) showed that this region is highly dynamic. (B) Structural comparison of KaiA135N with other receiver domains. Shown here are KaiA135N (Bi), the NtrC (1DC7) receiver domain (Bii), and the AmiR (1QO0 [PDB] , residues 11-131) receiver domain (Biii) at two mutually orthogonal views. Figures were prepared with SPOCK (38).

Figure 5.
Fig 5. Working model of KaiA protein function and its role in S. elongatus circadian timekeeping. CikA and other environmental sensors initiate signal transduction cascades that result in activation of the KaiA pseudo-receiver domain. This activation modulates the KaiA carboxyl-terminal domain's enhancement of the KaiC autophosphorylation rate. Thus, equilibria between KaiC phosphorylation states are perturbed. These states differentially control clock output, possibly through the SasA protein kinase. In this manner, a cycle of input, oscillation, and output can be established.

Figures were selected by an automated process.