5XC0

Crystal structure of an aromatic mutant (W6A) of an alkali thermostable GH10 Xylanase from Bacillus sp. NG-27

Summary for 5XC0

• Entry DOI: 10.2210/pdb5xc0/pdb
• Related: 5XC1
• Descriptor: Beta-xylanase, MAGNESIUM ION, SODIUM ION, ... (4 entities in total)
• Functional Keywords: tim barrel, xylanase, cryptic pocket, hydrolase
• Biological source: Bacillus sp. NG-27
• Total number of polymer chains: 2
• Total formula weight: 82091.21

Authors

Bansia, H.,Mahanta, P.,Ramakumar, S. (deposition date: 2017-03-21, release date: 2018-03-28, Last modification date: 2023-11-22)

Primary citation

Bansia, H.,Mahanta, P.,Yennawar, N.H.,Ramakumar, S.
Small Glycols Discover Cryptic Pockets on Proteins for Fragment-Based Approaches.
J.Chem.Inf.Model., 2021

PubMed Abstract: Cryptic pockets are visible in ligand-bound protein structures but are occluded in unbound structures. Utilizing these pockets in fragment-based drug-design provides an attractive option for proteins not tractable by classical binding sites. However, owing to their hidden nature, they are difficult to identify. Here, we show that small glycols find cryptic pockets on a diverse set of proteins. Initial crystallography experiments serendipitously revealed the ability of ethylene glycol, a small glycol, to identify a cryptic pocket on the W6A mutant of the RBSX protein (RBSX-W6A). Explicit-solvent molecular dynamics (MD) simulations of RBSX-W6A with the exposed state of the cryptic pocket (ethylene glycol removed) revealed closure of the pocket reiterating that the exposed state of cryptic pockets in general are unstable in the absence of ligands. Also, no change in the pocket was observed for simulations of RBSX-W6A with the occluded state of the cryptic pocket, suggesting that water molecules are not able to open the cryptic pocket. "Cryptic-pocket finding" potential of small glycols was then supported and generalized through additional crystallography experiments, explicit-cosolvent MD simulations, and protein data set construction and analysis. The cryptic pocket on RBSX-W6A was found again upon repeating the crystallography experiments with another small glycol, propylene glycol. Use of ethylene glycol as a probe molecule in cosolvent MD simulations led to the enhanced sampling of the exposed state of experimentally observed cryptic sites on a test set of two proteins (Niemann-Pick C2, Interleukin-2). Further, analyses of protein structures with validated cryptic sites showed that ethylene glycol molecules bind to sites on proteins (Bcl-xL, G-actin, myosin II, and glutamate receptor 2), which become apparent upon binding of biologically relevant ligands. Our study thus suggests potential application of the small glycols in experimental and computational fragment-based approaches to identify cryptic pockets in apparently undruggable and/or difficult targets, making these proteins amenable to drug-design strategies.

PubMed: 33570386
DOI: 10.1021/acs.jcim.0c01126

Experimental method

X-RAY DIFFRACTION (2.32 Å)