5m16

From Proteopedia

Structure of GH36 alpha-galactosidase from Thermotoga maritima in complex with a hydrolysed cyclopropyl carbasugar.

PDB ID 5m16

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Structural highlights

5m16 is a 1 chain structure with sequence from Thermotoga maritima. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.62Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AGAL_THEMA Hydrolyzes the short-chain alpha-galactosaccharides raffinose, melibiose and stachyose.^[1] ^[2]

Publication Abstract from PubMed

Glycoside hydrolases (GHs) have attracted considerable attention as targets for therapeutic agents, and thus mechanism-based inhibitors are of great interest. We report the first structural analysis of a carbocyclic mechanism-based GH inactivator, the results of which show that the two Michaelis complexes are in 2 H3 conformations. We also report the synthesis and reactivity of a fluorinated analogue and the structure of its covalently linked intermediate (flattened 2 H3 half-chair). We conclude that these inactivator reactions mainly involve motion of the pseudo-anomeric carbon atom, knowledge that should stimulate the design of new transition-state analogues for use as chemical biology tools.

Structural Snapshots for Mechanism-Based Inactivation of a Glycoside Hydrolase by Cyclopropyl Carbasugars.,Adamson C, Pengelly RJ, Shamsi Kazem Abadi S, Chakladar S, Draper J, Britton R, Gloster TM, Bennet AJ Angew Chem Int Ed Engl. 2016 Nov 21;55(48):14978-14982. doi:, 10.1002/anie.201607431. Epub 2016 Oct 26. PMID:27783466^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Borisova AS, Ivanen DR, Bobrov KS, Eneyskaya EV, Rychkov GN, Sandgren M, Kulminskaya AA, Sinnott ML, Shabalin KA. alpha-Galactobiosyl units: thermodynamics and kinetics of their formation by transglycosylations catalysed by the GH36 alpha-galactosidase from Thermotoga maritima. Carbohydr Res. 2015 Jan 12;401:115-21. doi: 10.1016/j.carres.2014.11.003. Epub, 2014 Nov 21. PMID:25486100 doi:http://dx.doi.org/10.1016/j.carres.2014.11.003
↑ Liebl W, Wagner B, Schellhase J. Properties of an alpha-galactosidase, and structure of its gene galA, within an alpha-and beta-galactoside utilization gene cluster of the hyperthermophilic bacterium Thermotoga maritima. Syst Appl Microbiol. 1998 Mar;21(1):1-11. PMID:9741105
↑ Adamson C, Pengelly RJ, Shamsi Kazem Abadi S, Chakladar S, Draper J, Britton R, Gloster TM, Bennet AJ. Structural Snapshots for Mechanism-Based Inactivation of a Glycoside Hydrolase by Cyclopropyl Carbasugars. Angew Chem Int Ed Engl. 2016 Nov 21;55(48):14978-14982. doi:, 10.1002/anie.201607431. Epub 2016 Oct 26. PMID:27783466 doi:http://dx.doi.org/10.1002/anie.201607431