6XIO

ADP-dependent kinase complex with fructose-6-phosphate and ADPbetaS

Summary for 6XIO

• Entry DOI: 10.2210/pdb6xio/pdb
• Descriptor: ADP-dependent phosphofructokinase, 5'-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE, 6-O-phosphono-beta-D-fructofuranose, ... (5 entities in total)
• Functional Keywords: ancestral protein reconstruction, adp-dependent sugar kinases family, glucokinase, phosphofructokinase, enzyme evolution, transferase
• Biological source: Methanosarcinales archaeon
• Total number of polymer chains: 1
• Total formula weight: 58496.43

Authors

Munoz, S.,Gonzalez-Ordenes, F.,Fuentes, N.,Maturana, P.,Herrera-Morande, A.,Villalobos, P.,Castro-Fernandez, V. (deposition date: 2020-06-20, release date: 2021-01-20, Last modification date: 2023-10-18)

Primary citation

Munoz, S.M.,Castro-Fernandez, V.,Guixe, V.
Structure of an ancestral ADP-dependent kinase with fructose-6P reveals key residues for binding, catalysis, and ligand-induced conformational changes.
J.Biol.Chem., 296:100219-100219, 2020

PubMed Abstract: ADP-dependent kinases were first described in archaea, although their presence has also been reported in bacteria and eukaryotes (human and mouse). This enzyme family comprises three substrate specificities; specific phosphofructokinases (ADP-PFKs), specific glucokinases (ADP-GKs), and bifunctional enzymes (ADP-PFK/GK). Although many structures are available for members of this family, none exhibits fructose-6-phosphate (F6P) at the active site. Using an ancestral enzyme, we obtain the first structure of an ADP-dependent kinase (AncMsPFK) with F6P at its active site. Key residues for sugar binding and catalysis were identified by alanine scanning, D36 being a critical residue for F6P binding and catalysis. However, this residue hinders glucose binding because its mutation to alanine converts the AncMsPFK enzyme into a specific ADP-GK. Residue K179 is critical for F6P binding, while residues N181 and R212 are also important for this sugar binding, but to a lesser extent. This structure also provides evidence for the requirement of both substrates (sugar and nucleotide) to accomplish the conformational change leading to a closed conformation. This suggests that AncMsPFK mainly populates two states (open and closed) during the catalytic cycle, as reported for specific ADP-PFK. This situation differs from that described for specific ADP-GK enzymes, where each substrate independently causes a sequential domain closure, resulting in three conformational states (open, semiclosed, and closed).

PubMed: 33839685
DOI: 10.1074/jbc.RA120.015376

Experimental method

X-RAY DIFFRACTION (3.12 Å)