7QVI | pdb_00007qvi

Fiber-forming RubisCO derived from ancestral sequence reconstruction and rational engineering

PDB DOI: https://doi.org/10.2210/pdb7QVI/pdb
EM Map EMD-14178: EMDB EMDataResource

Classification: LYASE
Organism(s): synthetic construct
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2022-01-21 Released: 2022-10-12
Deposition Author(s): Schulz, L., Zarzycki, J., Prinz, S., Schuller, J.M., Erb, T.J., Hochberg, G.K.A.
Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: 2D ARRAY
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Evolution of increased complexity and specificity at the dawn of form I Rubiscos.

Schulz, L., Guo, Z., Zarzycki, J., Steinchen, W., Schuller, J.M., Heimerl, T., Prinz, S., Mueller-Cajar, O., Erb, T.J., Hochberg, G.K.A.

(2022) Science 378: 155-160

PubMed: 36227987 Search on PubMed
DOI: https://doi.org/10.1126/science.abq1416
Primary Citation Related Structures:
7QSV, 7QSW, 7QSX, 7QSY, 7QSZ, 7QT1, 7QVI

PubMed Abstract:
The evolution of ribulose-1,5-bisphosphate carboxylase/oxygenases (Rubiscos) that discriminate strongly between their substrate carbon dioxide and the undesired side substrate dioxygen was an important event for photosynthetic organisms adapting to an oxygenated environment. We use ancestral sequence reconstruction to recapitulate this event. We show that Rubisco increased its specificity and carboxylation efficiency through the gain of an accessory subunit before atmospheric oxygen was present. Using structural and biochemical approaches, we retrace how this subunit was gained and became essential. Our work illuminates the emergence of an adaptation to rising ambient oxygen levels, provides a template for investigating the function of interactions that have remained elusive because of their essentiality, and sheds light on the determinants of specificity in Rubisco.

Organizational Affiliation

Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.

Macromolecule Content

Total Structure Weight: 825.24 kDa
Atom Count: 56,600
Modeled Residue Count: 7,128
Deposited Residue Count: 7,312
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RubisCO large subunit	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	457	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAP (Subject of Investigation/LOI) Query on CAP Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain CA [auth G] SDF format, chain GA [auth I] SDF format, chain IA [auth J] SDF format, chain MA [auth L] SDF format, chain OA [auth M] SDF format, chain Q [auth A] SDF format, chain QA [auth N] SDF format, chain W [auth D] SDF format, chain Y [auth E] SDF format, chain UA [auth P] SDF format, chain U [auth C] SDF format, chain SA [auth O] SDF format, chain S [auth B] SDF format, chain KA [auth K] SDF format, chain EA [auth H] MOL2 format, chain AA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain GA [auth I] MOL2 format, chain IA [auth J] MOL2 format, chain MA [auth L] MOL2 format, chain OA [auth M] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth N] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain UA [auth P] MOL2 format, chain U [auth C] MOL2 format, chain SA [auth O] MOL2 format, chain S [auth B] MOL2 format, chain KA [auth K] MOL2 format, chain EA [auth H] mmCIF format, chain AA [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain GA [auth I] mmCIF format, chain IA [auth J] mmCIF format, chain MA [auth L] mmCIF format, chain OA [auth M] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth N] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain UA [auth P] mmCIF format, chain U [auth C] mmCIF format, chain SA [auth O] mmCIF format, chain S [auth B] mmCIF format, chain KA [auth K] mmCIF format, chain EA [auth H]	AA [auth F] CA [auth G] EA [auth H] GA [auth I] IA [auth J] AA [auth F], CA [auth G], EA [auth H], GA [auth I], IA [auth J], KA [auth K], MA [auth L], OA [auth M], Q [auth A], QA [auth N], S [auth B], SA [auth O], U [auth C], UA [auth P], W [auth D], Y [auth E]	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE C₆ H₁₄ O₁₃ P₂ ITHCSGCUQDMYAI-ZMIZWQJLSA-N		Interactions Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain IA [auth J] Focus chain KA [auth K] Focus chain MA [auth L] Focus chain OA [auth M] Focus chain Q [auth A] Focus chain QA [auth N] Focus chain S [auth B] Focus chain SA [auth O] Focus chain U [auth C] Focus chain UA [auth P] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain IA [auth J] Focus chain KA [auth K] Focus chain MA [auth L] Focus chain OA [auth M] Focus chain Q [auth A] Focus chain QA [auth N] Focus chain S [auth B] Focus chain SA [auth O] Focus chain U [auth C] Focus chain UA [auth P] Focus chain W [auth D] Focus chain Y [auth E]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain DA [auth G] SDF format, chain FA [auth H] SDF format, chain HA [auth I] SDF format, chain LA [auth K] SDF format, chain NA [auth L] SDF format, chain PA [auth M] SDF format, chain RA [auth N] SDF format, chain T [auth B] SDF format, chain TA [auth O] SDF format, chain V [auth C] SDF format, chain Z [auth E] SDF format, chain X [auth D] SDF format, chain VA [auth P] SDF format, chain R [auth A] SDF format, chain JA [auth J] MOL2 format, chain BA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain HA [auth I] MOL2 format, chain LA [auth K] MOL2 format, chain NA [auth L] MOL2 format, chain PA [auth M] MOL2 format, chain RA [auth N] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth O] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth E] MOL2 format, chain X [auth D] MOL2 format, chain VA [auth P] MOL2 format, chain R [auth A] MOL2 format, chain JA [auth J] mmCIF format, chain BA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain HA [auth I] mmCIF format, chain LA [auth K] mmCIF format, chain NA [auth L] mmCIF format, chain PA [auth M] mmCIF format, chain RA [auth N] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth O] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth E] mmCIF format, chain X [auth D] mmCIF format, chain VA [auth P] mmCIF format, chain R [auth A] mmCIF format, chain JA [auth J]	BA [auth F] DA [auth G] FA [auth H] HA [auth I] JA [auth J] BA [auth F], DA [auth G], FA [auth H], HA [auth I], JA [auth J], LA [auth K], NA [auth L], PA [auth M], R [auth A], RA [auth N], T [auth B], TA [auth O], V [auth C], VA [auth P], X [auth D], Z [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain JA [auth J] Focus chain LA [auth K] Focus chain NA [auth L] Focus chain PA [auth M] Focus chain R [auth A] Focus chain RA [auth N] Focus chain T [auth B] Focus chain TA [auth O] Focus chain V [auth C] Focus chain VA [auth P] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain JA [auth J] Focus chain LA [auth K] Focus chain NA [auth L] Focus chain PA [auth M] Focus chain R [auth A] Focus chain RA [auth N] Focus chain T [auth B] Focus chain TA [auth O] Focus chain V [auth C] Focus chain VA [auth P] Focus chain X [auth D] Focus chain Z [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS