Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C6  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C6  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 127.50 kDa 
• Atom Count: 6427 
• Modelled Residue Count: 801 
• Deposited Residue Count: 1140 
• Unique protein chains: 1

6L1Q

Crystal structure of AfCbbQ2, a MoxR AAA+-ATPase and CbbQO-type Rubisco activase from Acidithiobacillus ferrooxidans

• PDB DOI: 10.2210/pdb6L1Q/pdb

• Classification: CHAPERONE
• Organism(s): Acidithiobacillus ferrooxidans ATCC 23270
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-09-30 Released: 2019-12-18 
• Deposition Author(s): Ye, F.Z., Tsai, Y.C.C., Mueller-Cajar, O., Gao, Y.G.
• Funding Organization(s): Ministry of Education (Singapore)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.238 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

Literature

Insights into the mechanism and regulation of the CbbQO-type Rubisco activase, a MoxR AAA+ ATPase.

Tsai, Y.C., Ye, F., Liew, L., Liu, D., Bhushan, S., Gao, Y.G., Mueller-Cajar, O.

(2020) Proc Natl Acad Sci U S A 117: 381-387

• PubMed: 31848241 
• DOI: 10.1073/pnas.1911123117
• Primary Citation of Related Structures:  
  6L1Q


• PubMed Abstract: 
  

The vast majority of biological carbon dioxide fixation relies on the function of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco). In most cases the enzyme exhibits a tendency to become inhibited by its substrate RuBP and other sugar phosphates. The inhibition is counteracted by diverse molecular chaperones known as Rubisco activases (Rcas). In some chemoautotrophic bacteria, the CbbQO-type Rca Q2O2 repairs inhibited active sites of hexameric form II Rubisco. The 2.2-Å crystal structure of the MoxR AAA+ protein CbbQ2 from Acidithiobacillus ferrooxidans reveals the helix 2 insert (H2I) that is critical for Rca function and forms the axial pore of the CbbQ hexamer. Negative-stain electron microscopy shows that the essential CbbO adaptor protein binds to the conserved, concave side of the CbbQ2 hexamer. Site-directed mutagenesis supports a model in which adenosine 5'-triphosphate (ATP)-powered movements of the H2I are transmitted to CbbO via the concave residue L85. The basal ATPase activity of Q2O2 Rca is repressed but strongly stimulated by inhibited Rubisco. The characterization of multiple variants where this repression is released indicates that binding of inhibited Rubisco to the C-terminal CbbO VWA domain initiates a signal toward the CbbQ active site that is propagated via elements that include the CbbQ α4-β4 loop, pore loop 1, and the presensor 1-β hairpin (PS1-βH). Detailed mechanistic insights into the enzyme repair chaperones of the highly diverse CO ₂ fixation machinery of Proteobacteria will facilitate their successful implementation in synthetic biology ventures.

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Organizational Affiliation: 

Nanyang Technological University Institute of Structural Biology, Nanyang Technological University, 636921, Singapore.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CbbQ protein	B [auth A], C [auth B], A [auth C]	380	Acidithiobacillus ferrooxidans ATCC 23270	Mutation(s): 0  Gene Names: cbbQ-2, AFE_2156
UniProt
Find proteins for B7J5E4 (Acidithiobacillus ferrooxidans (strain ATCC 23270 / DSM 14882 / CIP 104768 / NCIMB 8455)) Explore B7J5E4  Go to UniProtKB:  B7J5E4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	D [auth C], F [auth A], H [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4	E [auth C], G [auth A], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.238 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.753	α = 90
b = 167.753	β = 90
c = 48.291	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-09-30 
• Released Date: 2019-12-18 
Deposition Author(s): Ye, F.Z., Tsai, Y.C.C., Mueller-Cajar, O., Gao, Y.G.

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Funding Organization	Location	Grant Number
Ministry of Education (Singapore)	Singapore	MOE2016-T2-02-088

Revision History  

• Version 1.0: 2019-12-18
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Database references
• Version 1.2: 2020-01-22
  Changes: Database references