8IO6

Cryo-EM structure of phosphoketolase from Bifidobacterium longum in octameric assembly

Summary for 8IO6

• Entry DOI: 10.2210/pdb8io6/pdb
• EMDB information: 35609
• Descriptor: Xylulose5phosphatefructose6phosphate phosphoketolase, THIAMINE DIPHOSPHATE, MAGNESIUM ION (3 entities in total)
• Functional Keywords: carbon metabolism, tpp-dependent enzyme, cytosolic protein
• Biological source: Bifidobacterium longum subsp. longum F8
• Total number of polymer chains: 8
• Total formula weight: 744565.95

Authors

Chang, C.-W.,Tsai, M.-D. (deposition date: 2023-03-10, release date: 2023-06-28, Last modification date: 2023-11-15)

Primary citation

Lu, K.J.,Chang, C.W.,Wang, C.H.,Chen, F.Y.,Huang, I.Y.,Huang, P.H.,Yang, C.H.,Wu, H.Y.,Wu, W.J.,Hsu, K.C.,Ho, M.C.,Tsai, M.D.,Liao, J.C.
An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria.
Nat Metab, 5:1111-1126, 2023

PubMed Abstract: Regulation of CO fixation in cyanobacteria is important both for the organism and global carbon balance. Here we show that phosphoketolase in Synechococcus elongatus PCC7942 (SeXPK) possesses a distinct ATP-sensing mechanism, where a drop in ATP level allows SeXPK to divert precursors of the RuBisCO substrate away from the Calvin-Benson-Bassham cycle. Deleting the SeXPK gene increased CO fixation particularly during light-dark transitions. In high-density cultures, the Δxpk strain showed a 60% increase in carbon fixation and unexpectedly resulted in sucrose secretion without any pathway engineering. Using cryo-EM analysis, we discovered that these functions were enabled by a unique allosteric regulatory site involving two subunits jointly binding two ATP, which constantly suppresses the activity of SeXPK until the ATP level drops. This magnesium-independent ATP allosteric site is present in many species across all three domains of life, where it may also play important regulatory functions.

PubMed: 37349485
DOI: 10.1038/s42255-023-00831-w

Experimental method

ELECTRON MICROSCOPY (2.68 Å)