6LXV

Cryo-EM structure of phosphoketolase from Bifidobacterium longum

Summary for 6LXV

• Entry DOI: 10.2210/pdb6lxv/pdb
• Related: 3ai7
• EMDB information: 30007
• Descriptor: Phosphoketolase, THIAMINE DIPHOSPHATE, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: lyase, ketolase, thiamine diphosphate, octamer, bifidobacterium longum, lyase activity
• Biological source: Bifidobacterium longum subsp. longum F8
• Total number of polymer chains: 8
• Total formula weight: 751323.26

Authors

Nakata, K.,Miyazaki, N.,Yamaguchi, H.,Hirose, M.,Miyano, H.,Mizukoshi, T.,Kashiwagi, T.,Iwasaki, K. (deposition date: 2020-02-12, release date: 2021-02-17, Last modification date: 2024-05-29)

Primary citation

Nakata, K.,Miyazaki, N.,Yamaguchi, H.,Hirose, M.,Kashiwagi, T.,Kutumbarao, N.H.V.,Miyashita, O.,Tama, F.,Miyano, H.,Mizukoshi, T.,Iwasaki, K.
High-resolution structure of phosphoketolase from Bifidobacterium longum determined by cryo-EM single-particle analysis.
J.Struct.Biol., 214:107842-107842, 2022

PubMed Abstract: In bifidobacteria, phosphoketolase (PKT) plays a key role in the central hexose fermentation pathway called "bifid shunt." The three-dimensional structure of PKT from Bifidobacterium longum with co-enzyme thiamine diphosphate (ThDpp) was determined at 2.1 Å resolution by cryo-EM single-particle analysis using 196,147 particles to build up the structural model of a PKT octamer related by D symmetry. Although the cryo-EM structure of PKT was almost identical to the X-ray crystal structure previously determined at 2.2 Å resolution, several interesting structural features were observed in the cryo-EM structure. Because this structure was solved at relatively high resolution, it was observed that several amino acid residues adopt multiple conformations. Among them, Q546-D547-H548-N549 (the QN-loop) demonstrate the largest structural change, which seems to be related to the enzymatic function of PKT. The QN-loop is at the entrance to the substrate binding pocket. The minor conformer of the QN-loop is similar to the conformation of the QN-loop in the crystal structure. The major conformer is located further from ThDpp than the minor conformer. Interestingly, the major conformer in the cryo-EM structure of PKT resembles the corresponding loop structure of substrate-bound Escherichia coli transketolase. That is, the minor and major conformers may correspond to "closed" and "open" states for substrate access, respectively. Moreover, because of the high-resolution analysis, many water molecules were observed in the cryo-EM structure of PKT. Structural features of the water molecules in the cryo-EM structure are discussed and compared with water molecules observed in the crystal structure.

PubMed: 35181457
DOI: 10.1016/j.jsb.2022.107842

Experimental method

ELECTRON MICROSCOPY (2.1 Å)