6HAF

Pyruvate oxidase variant E59Q from L. plantarum in complex with phosphate

Summary for 6HAF

• Entry DOI: 10.2210/pdb6haf/pdb
• Related: 4kgd
• Descriptor: Pyruvate oxidase, FLAVIN-ADENINE DINUCLEOTIDE, POTASSIUM ION, ... (8 entities in total)
• Functional Keywords: carbanion, structure activity relationship, oxidation-reduction, umpolung, thiamine diphosphate, reaction intermediate, flavin adenine dinucleotide, oxidoreductase
• Biological source: Lactobacillus plantarum
• Total number of polymer chains: 2
• Total formula weight: 136255.23

Authors

Funk, L.M.,Sautner, V.,Tittmann, K. (deposition date: 2018-08-07, release date: 2019-08-21, Last modification date: 2024-05-15)

Primary citation

Dai, S.,Funk, L.M.,von Pappenheim, F.R.,Sautner, V.,Paulikat, M.,Schroder, B.,Uranga, J.,Mata, R.A.,Tittmann, K.
Low-barrier hydrogen bonds in enzyme cooperativity.
Nature, 573:609-613, 2019

PubMed Abstract: The underlying molecular mechanisms of cooperativity and allosteric regulation are well understood for many proteins, with haemoglobin and aspartate transcarbamoylase serving as prototypical examples. The binding of effectors typically causes a structural transition of the protein that is propagated through signalling pathways to remote sites and involves marked changes on the tertiary and sometimes even the quaternary level. However, the origin of these signals and the molecular mechanism of long-range signalling at an atomic level remain unclear. The different spatial scales and timescales in signalling pathways render experimental observation challenging; in particular, the positions and movement of mobile protons cannot be visualized by current methods of structural analysis. Here we report the experimental observation of fluctuating low-barrier hydrogen bonds as switching elements in cooperativity pathways of multimeric enzymes. We have observed these low-barrier hydrogen bonds in ultra-high-resolution X-ray crystallographic structures of two multimeric enzymes, and have validated their assignment using computational calculations. Catalytic events at the active sites switch between low-barrier hydrogen bonds and ordinary hydrogen bonds in a circuit that consists of acidic side chains and water molecules, transmitting a signal through the collective repositioning of protons by behaving as an atomistic Newton's cradle. The resulting communication synchronizes catalysis in the oligomer. Our studies provide several lines of evidence and a working model for not only the existence of low-barrier hydrogen bonds in proteins, but also a connection to enzyme cooperativity. This finding suggests new principles of drug and enzyme design, in which sequences of residues can be purposefully included to enable long-range communication and thus the regulation of engineered biomolecules.

PubMed: 31534226
DOI: 10.1038/s41586-019-1581-9

Experimental method

X-RAY DIFFRACTION (1.3 Å)