7C8H

Ambient temperature structure of Bifidobacterium longum phosphoketolase with thiamine diphosphate

Summary for 7C8H

• Entry DOI: 10.2210/pdb7c8h/pdb
• Descriptor: Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase, THIAMINE DIPHOSPHATE, CALCIUM ION, ... (7 entities in total)
• Functional Keywords: xfel-sfx, ambient temperature, aldehyde-lyase activity, carbohydrate metabolic process, thiamine-diphosphate (thdpp), lyase
• Biological source: Bifidobacterium longum
• Total number of polymer chains: 8
• Total formula weight: 752257.88

Authors

Nakata, K.,Kashiwagi, T.,Nango, E.,Miyano, H.,Mizukoshi, T.,Iwata, S. (deposition date: 2020-06-01, release date: 2021-06-02, Last modification date: 2023-11-29)

Primary citation

Nakata, K.,Kashiwagi, T.,Kunishima, N.,Naitow, H.,Matsuura, Y.,Miyano, H.,Mizukoshi, T.,Tono, K.,Yabashi, M.,Nango, E.,Iwata, S.
Ambient temperature structure of phosphoketolase from Bifidobacterium longum determined by serial femtosecond X-ray crystallography.
Acta Crystallogr D Struct Biol, 79:290-303, 2023

PubMed Abstract: Phosphoketolase and transketolase are thiamine diphosphate-dependent enzymes and play a central role in the primary metabolism of bifidobacteria: the bifid shunt. The enzymes both catalyze phosphorolytic cleavage of xylulose 5-phosphate or fructose 6-phosphate in the first reaction step, but possess different substrate specificity in the second reaction step, where phosphoketolase and transketolase utilize inorganic phosphate (P) and D-ribose 5-phosphate, respectively, as the acceptor substrate. Structures of Bifidobacterium longum phosphoketolase holoenzyme and its complex with a putative inhibitor, phosphoenolpyruvate, were determined at 2.5 Å resolution by serial femtosecond crystallography using an X-ray free-electron laser. In the complex structure, phosphoenolpyruvate was present at the entrance to the active-site pocket and plugged the channel to thiamine diphosphate. The phosphate-group position of phosphoenolpyruvate coincided well with those of xylulose 5-phosphate and fructose 6-phosphate in the structures of their complexes with transketolase. The most striking structural change was observed in a loop consisting of Gln546-Asp547-His548-Asn549 (the QN-loop) at the entrance to the active-site pocket. Contrary to the conformation of the QN-loop that partially covers the entrance to the active-site pocket (`closed form') in the known crystal structures, including the phosphoketolase holoenzyme and its complexes with reaction intermediates, the QN-loop in the current ambient structures showed a more compact conformation with a widened entrance to the active-site pocket (`open form'). In the phosphoketolase reaction, the `open form' QN-loop may play a role in providing the binding site for xylulose 5-phosphate or fructose 6-phosphate in the first step, and the `closed form' QN-loop may help confer specificity for P in the second step.

PubMed: 36974963
DOI: 10.1107/S2059798323001638

Experimental method

X-RAY DIFFRACTION (2.5 Å)