8ZN5 | pdb_00008zn5

Crystal Structure of Designed Clock Protein KaiC

PDB DOI: https://doi.org/10.2210/pdb8ZN5/pdb

Classification: TRANSFERASE
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-05-26 Released: 2025-04-16
Deposition Author(s): Furuike, Y., Akiyama, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.329 (Depositor)
R-Value Work:
0.280 (Depositor)
R-Value Observed:
0.283 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Evolutionary origins of self-sustained Kai protein circadian oscillators in cyanobacteria.

Mukaiyama, A., Furuike, Y., Ito-Miwa, K., Onoue, Y., Horiuchi, K., Kondo, K., Yamashita, E., Akiyama, S.

(2025) Nat Commun 16: 4541-4541

PubMed: 40374681 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-59908-7
Primary Citation Related Structures:
8ZN5, 8ZN6, 8ZN7

PubMed Abstract:
Light-dark cycles affect photosynthetic efficiency in autotrophic cyanobacteria; therefore, determining whether ancient cyanobacteria possessed a self-sustained circadian clock when oxygenic photosynthetic systems were established is an important issue in chronobiology. Here we examine the oscillation of the clock protein KaiC in modern cyanobacteria, as well as the function and structure of ancestral Kai proteins, to determine the evolutionary origin of the self-sustained Kai-protein oscillators. The results show that the oldest double-domain KaiC in ancestral bacteria lacks the factors functionally and structurally essential for rhythmicity. The ancestral Kai proteins have acquired these factors through molecular evolution that occurred around Global Oxidation and Snowball Earth events, and are eventually inherited as a self-sustained circadian oscillator by the most recent common ancestor of cyanobacteria capable of oxygenic photosynthesis. This autonomous Kai protein oscillator is further inherited by most freshwater and marine cyanobacteria present today as an autotrophic basis for time-optimal acquisition and consumption of energy from oxygenic photosynthesis.

Organizational Affiliation

Department of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji, 910-1195, Japan. amukai@fpu.ac.jp.

Macromolecule Content

Total Structure Weight: 709.71 kDa
Atom Count: 36,725
Modeled Residue Count: 5,370
Deposited Residue Count: 6,216
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KaiC	A [auth B] B [auth C] C [auth F] D [auth A] E [auth D] A [auth B], B [auth C], C [auth F], D [auth A], E [auth D], F [auth E], G, H, I [auth K], J [auth L], K [auth I], L [auth J]	518	synthetic construct	Mutation(s): 0 EC: 2.7.11.1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain AB [auth I] SDF format, chain BB [auth I] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EB [auth J] SDF format, chain FB [auth J] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain KA [auth G] SDF format, chain LA [auth G] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain OA [auth H] SDF format, chain PA [auth H] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain SA [auth K] SDF format, chain TA [auth K] SDF format, chain U [auth F] SDF format, chain V [auth F] SDF format, chain WA [auth L] SDF format, chain XA [auth L] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AB [auth I] MOL2 format, chain BB [auth I] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EB [auth J] MOL2 format, chain FB [auth J] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth G] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain OA [auth H] MOL2 format, chain PA [auth H] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain SA [auth K] MOL2 format, chain TA [auth K] MOL2 format, chain U [auth F] MOL2 format, chain V [auth F] MOL2 format, chain WA [auth L] MOL2 format, chain XA [auth L] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AB [auth I] mmCIF format, chain BB [auth I] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EB [auth J] mmCIF format, chain FB [auth J] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain KA [auth G] mmCIF format, chain LA [auth G] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain OA [auth H] mmCIF format, chain PA [auth H] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain SA [auth K] mmCIF format, chain TA [auth K] mmCIF format, chain U [auth F] mmCIF format, chain V [auth F] mmCIF format, chain WA [auth L] mmCIF format, chain XA [auth L] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AB [auth I] BB [auth I] CA [auth D] DA [auth D] EB [auth J] AB [auth I], BB [auth I], CA [auth D], DA [auth D], EB [auth J], FB [auth J], GA [auth E], HA [auth E], KA [auth G], LA [auth G], M [auth B], N [auth B], OA [auth H], PA [auth H], Q [auth C], R [auth C], SA [auth K], TA [auth K], U [auth F], V [auth F], WA [auth L], XA [auth L], Y [auth A], Z [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AB [auth I] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EB [auth J] Focus chain FB [auth J] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain M [auth B] Focus chain N [auth B] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain Q [auth C] Focus chain R [auth C] Focus chain SA [auth K] Focus chain TA [auth K] Focus chain U [auth F] Focus chain V [auth F] Focus chain WA [auth L] Focus chain XA [auth L] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AB [auth I] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EB [auth J] Focus chain FB [auth J] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain M [auth B] Focus chain N [auth B] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain Q [auth C] Focus chain R [auth C] Focus chain SA [auth K] Focus chain TA [auth K] Focus chain U [auth F] Focus chain V [auth F] Focus chain WA [auth L] Focus chain XA [auth L] Focus chain Y [auth A] Focus chain Z [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CB [auth I] SDF format, chain DB [auth I] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GB [auth J] SDF format, chain HB [auth J] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain MA [auth G] SDF format, chain NA [auth G] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain QA [auth H] SDF format, chain RA [auth H] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain UA [auth K] SDF format, chain VA [auth K] SDF format, chain W [auth F] SDF format, chain X [auth F] SDF format, chain YA [auth L] SDF format, chain ZA [auth L] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CB [auth I] MOL2 format, chain DB [auth I] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GB [auth J] MOL2 format, chain HB [auth J] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain MA [auth G] MOL2 format, chain NA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth H] MOL2 format, chain RA [auth H] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain UA [auth K] MOL2 format, chain VA [auth K] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F] MOL2 format, chain YA [auth L] MOL2 format, chain ZA [auth L] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CB [auth I] mmCIF format, chain DB [auth I] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GB [auth J] mmCIF format, chain HB [auth J] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain MA [auth G] mmCIF format, chain NA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain QA [auth H] mmCIF format, chain RA [auth H] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain UA [auth K] mmCIF format, chain VA [auth K] mmCIF format, chain W [auth F] mmCIF format, chain X [auth F] mmCIF format, chain YA [auth L] mmCIF format, chain ZA [auth L]	AA [auth A] BA [auth A] CB [auth I] DB [auth I] EA [auth D] AA [auth A], BA [auth A], CB [auth I], DB [auth I], EA [auth D], FA [auth D], GB [auth J], HB [auth J], IA [auth E], JA [auth E], MA [auth G], NA [auth G], O [auth B], P [auth B], QA [auth H], RA [auth H], S [auth C], T [auth C], UA [auth K], VA [auth K], W [auth F], X [auth F], YA [auth L], ZA [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CB [auth I] Focus chain DB [auth I] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GB [auth J] Focus chain HB [auth J] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain O [auth B] Focus chain P [auth B] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain S [auth C] Focus chain T [auth C] Focus chain UA [auth K] Focus chain VA [auth K] Focus chain W [auth F] Focus chain X [auth F] Focus chain YA [auth L] Focus chain ZA [auth L] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CB [auth I] Focus chain DB [auth I] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GB [auth J] Focus chain HB [auth J] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain O [auth B] Focus chain P [auth B] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain S [auth C] Focus chain T [auth C] Focus chain UA [auth K] Focus chain VA [auth K] Focus chain W [auth F] Focus chain X [auth F] Focus chain YA [auth L] Focus chain ZA [auth L]