4NSV

Lysobacter enzymogenes lysc endoproteinase K30R mutant covalently inhibited by TLCK

Summary for 4NSV

• Entry DOI: 10.2210/pdb4nsv/pdb
• Related: 4NSY
• Related PRD ID: PRD_001217
• Descriptor: Lysyl endopeptidase, N-[(2S,3S)-7-amino-1-chloro-2-hydroxyheptan-3-yl]-4-methylbenzenesulfonamide (Bound Form), SULFATE ION, ... (5 entities in total)
• Functional Keywords: hydrolase, endoproteinase, aromatic stack, atomic resolution, serine protease, catalytic triad, covalent inhibition, tlck;, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Lysobacter enzymogenes
• Cellular location: Secreted: Q7M135
• Total number of polymer chains: 2
• Total formula weight: 58491.80

Authors

Asztalos, P.,Muller, A.,Holke, W.,Sobek, H.,Rudolph, M.G. (deposition date: 2013-11-29, release date: 2014-04-23, Last modification date: 2024-11-20)

Primary citation

Asztalos, P.,Muller, A.,Holke, W.,Sobek, H.,Rudolph, M.G.
Atomic resolution structure of a lysine-specific endoproteinase from Lysobacter enzymogenes suggests a hydroxyl group bound to the oxyanion hole.
Acta Crystallogr.,Sect.D, 70:1832-1843, 2014

PubMed Abstract: Lysobacter enzymogenes lysyl endoproteinase (LysC) is a trypsin-type serine protease with a high pH optimum that hydrolyses all Lys-Xaa peptide bonds. The high specificity of LysC renders it useful for biotechnological purposes. The K30R variant of a related lysyl endoproteinase from Achromobacter lyticus has favourable enzymatic properties that might be transferrable to LysC. To visualize structural differences in the substrate-binding sites, the crystal structures of wild-type and the K30R variant of LysC were determined. The mutation is located at a distance of 12 Å from the catalytic triad and subtly changes the surface properties of the substrate-binding site. The high pH optimum of LysC can be attributed to electrostatic effects of an aromatic Tyr/His stack on the catalytic aspartate and is a general feature of this enzyme subfamily. LysC crystals in complex with the covalent inhibitor N(α)-p-tosyl-lysyl chloromethylketone yielded data to 1.1 and 0.9 Å resolution, resulting in unprecedented precision of the active and substrate-binding sites for this enzyme subfamily. Error estimates on bond lengths and difference electron density indicate that instead of the expected oxyanion a hydroxyl group binds to the partially solvent-exposed oxyanion hole. Protonation of the alkoxide catalytic intermediate might be a recurring feature during serine protease catalysis.

PubMed: 25004961
DOI: 10.1107/S1399004714008463

Experimental method

X-RAY DIFFRACTION (0.9 Å)