8DOT

Structure of a methane clathrate binding protein

Summary for 8DOT

• Entry DOI: 10.2210/pdb8dot/pdb
• Descriptor: methane clathrate binding protein, TETRAETHYLENE GLYCOL (2 entities in total)
• Functional Keywords: methane, clathrate, subsurface, metagenome, antifreeze protein
• Biological source: marine sediment metagenome
• Total number of polymer chains: 1
• Total formula weight: 47377.48

Authors

Huard, D.J.E.,Lieberman, R.L.,Glass, J.B. (deposition date: 2022-07-14, release date: 2023-09-13)

Primary citation

Huard, D.J.E.,Johnson, A.M.,Fan, Z.,Kenney, L.G.,Xu, M.,Drori, R.,Gumbart, J.C.,Dai, S.,Lieberman, R.L.,Glass, J.B.
Molecular basis for inhibition of methane clathrate growth by a deep subsurface bacterial protein.
Pnas Nexus, 2:pgad268-pgad268, 2023

PubMed Abstract: Methane clathrates on continental margins contain the largest stores of hydrocarbons on Earth, yet the role of biomolecules in clathrate formation and stability remains almost completely unknown. Here, we report new methane clathrate-binding proteins (CbpAs) of bacterial origin discovered in metagenomes from gas clathrate-bearing ocean sediments. CbpAs show similar suppression of methane clathrate growth as the commercial gas clathrate inhibitor polyvinylpyrrolidone and inhibit clathrate growth at lower concentrations than antifreeze proteins (AFPs) previously tested. Unlike AFPs, CbpAs are selective for clathrate over ice. CbpA adopts a nonglobular, extended structure with an exposed hydrophobic surface, and, unexpectedly, its TxxxAxxxAxx motif common to AFPs is buried and not involved in clathrate binding. Instead, simulations and mutagenesis suggest a bipartite interaction of CbpAs with methane clathrate, with the pyrrolidine ring of a highly conserved proline residue mediating binding by filling empty clathrate cages. The discovery that CbpAs exert such potent control on methane clathrate properties implies that biomolecules from native sediment bacteria may be important for clathrate stability and habitability.

PubMed: 37644917
DOI: 10.1093/pnasnexus/pgad268

Experimental method

X-RAY DIFFRACTION (3.05 Å)