6GHL

cyanobacterial GAPDH with full-length CP12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of light-induced redox regulation in the Calvin-Benson cycle in cyanobacteria.

McFarlane, C.R.Shah, N.R.Kabasakal, B.V.Echeverria, B.Cotton, C.A.R.Bubeck, D.Murray, J.W.

(2019) Proc Natl Acad Sci U S A 116: 20984-20990

  • DOI: 10.1073/pnas.1906722116
  • Primary Citation of Related Structures:  
    6GFP, 6GFO, 6GFR, 6GFQ, 6GG7, 6GHR, 6GHL, 6GVE

  • PubMed Abstract: 
  • Plants, algae, and cyanobacteria fix carbon dioxide to organic carbon with the Calvin-Benson (CB) cycle. Phosphoribulokinase (PRK) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) are essential CB-cycle enzymes that control substrate availability for the carboxylation enzyme Rubisco ...

    Plants, algae, and cyanobacteria fix carbon dioxide to organic carbon with the Calvin-Benson (CB) cycle. Phosphoribulokinase (PRK) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) are essential CB-cycle enzymes that control substrate availability for the carboxylation enzyme Rubisco. PRK consumes ATP to produce the Rubisco substrate ribulose bisphosphate (RuBP). GAPDH catalyzes the reduction step of the CB cycle with NADPH to produce the sugar glyceraldehyde 3-phosphate (GAP), which is used for regeneration of RuBP and is the main exit point of the cycle. GAPDH and PRK are coregulated by the redox state of a conditionally disordered protein CP12, which forms a ternary complex with both enzymes. However, the structural basis of CB-cycle regulation by CP12 is unknown. Here, we show how CP12 modulates the activity of both GAPDH and PRK. Using thermophilic cyanobacterial homologs, we solve crystal structures of GAPDH with different cofactors and CP12 bound, and the ternary GAPDH-CP12-PRK complex by electron cryo-microscopy, we reveal that formation of the N-terminal disulfide preorders CP12 prior to binding the PRK active site, which is resolved in complex with CP12. We find that CP12 binding to GAPDH influences substrate accessibility of all GAPDH active sites in the binary and ternary inhibited complexes. Our structural and biochemical data explain how CP12 integrates responses from both redox state and nicotinamide dinucleotide availability to regulate carbon fixation.


    Organizational Affiliation

    Department of Life Sciences, Imperial College London, SW7 2AZ, United Kingdom d.bubeck@imperial.ac.uk j.w.murray@imperial.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CP12 polypeptideB [auth E], A [auth F]77Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: cp12
UniProt
Find proteins for Q8DHX3 (Thermosynechococcus elongatus (strain BP-1))
Explore Q8DHX3 
Go to UniProtKB:  Q8DHX3
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenaseC [auth A], D [auth B], E [auth C], F [auth D]339Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: tll1466
EC: 1.2.1
UniProt
Find proteins for Q8DIW5 (Thermosynechococcus elongatus (strain BP-1))
Explore Q8DIW5 
Go to UniProtKB:  Q8DIW5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
G [auth A], H [auth B], I [auth C], K [auth D]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
MLI
Query on MLI

Download Ideal Coordinates CCD File 
J [auth C]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.79α = 90
b = 138.801β = 90
c = 139.772γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J014575/1

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references