6HZL

Crystal structure of redox-inhibited phosphoribulokinase from Synechococcus sp. (strain PCC 6301), osmate derivative

• PDB DOI: https://doi.org/10.2210/pdb6HZL/pdb

• Classification: TRANSFERASE
• Organism(s): Synechococcus elongatus PCC 6301
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-23 Released: 2019-03-27 
• Deposition Author(s): Wilson, R.H., Bracher, A., Hartl, F.U., Hayer-Hartl, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.259 
• R-Value Work: 0.235 
• R-Value Observed: 0.236 

Literature

Crystal structure of phosphoribulokinase from Synechococcus sp. strain PCC 6301.

Wilson, R.H., Hayer-Hartl, M., Bracher, A.

(2019) Acta Crystallogr F Struct Biol Commun 75: 278-289

• PubMed: 30950829 
• DOI: https://doi.org/10.1107/S2053230X19002693
• Primary Citation of Related Structures:  
  6HZK, 6HZL


• PubMed Abstract: 
  

  Phosphoribulokinase (PRK) catalyses the ATP-dependent phosphorylation of ribulose 5-phosphate to give ribulose 1,5-bisphosphate. Regulation of this reaction in response to light controls carbon fixation during photosynthesis. Here, the crystal structure of PRK from the cyanobacterium Synechococcus sp. strain PCC 6301 is presented. The enzyme is dimeric and has an α/β-fold with an 18-stranded β-sheet at its core. Interestingly, a disulfide bond is found between Cys40 and the P-loop residue Cys18, revealing the structural basis for the redox inactivation of PRK activity. A second disulfide bond appears to rigidify the dimer interface and may thereby contribute to regulation by the adaptor protein CP12 and glyceraldehyde-3-phosphate dehydrogenase.

---

Organizational Affiliation: 

Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 75.9 kDa 
• Atom Count: 4,957 
• Modelled Residue Count: 624 
• Deposited Residue Count: 666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribulokinase	A, B	333	Synechococcus elongatus PCC 6301	Mutation(s): 0  Gene Names: prk, syc0567_d EC: 2.7.1.19
UniProt
Find proteins for A0A0H3K6J7 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1)) Explore A0A0H3K6J7  Go to UniProtKB:  A0A0H3K6J7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OS	C [auth A], D [auth A]	OSMIUM ION Os XQBKHDFIPARBOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.259 
• R-Value Work: 0.235 
• R-Value Observed: 0.236 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.432	α = 90
b = 141.432	β = 90
c = 206.563	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
HKL2Map	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Wilson, R.H., Bracher, A., Hartl, F.U., Hayer-Hartl, M.

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2019-04-10
  Changes: Data collection, Database references
• Version 1.2: 2019-04-17
  Changes: Data collection, Database references