6T5Z

Crystal structure of an AA10 LPMO from Photorhabdus luminescens

Summary for 6T5Z

• Entry DOI: 10.2210/pdb6t5z/pdb
• Descriptor: Chitin-binding type-4 domain-containing protein, COPPER (II) ION (3 entities in total)
• Functional Keywords: lytic polysaccharide monooxygenase, copper metalloenzyme, chitin, oxidoreductase
• Biological source: Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)
• Total number of polymer chains: 3
• Total formula weight: 59189.92

Authors

Munzone, A.,El Kerdi, B.,Reglier, M.,Royant, A.,Simaan, A.J.,Decroos, C. (deposition date: 2019-10-17, release date: 2020-01-15, Last modification date: 2024-01-24)

Primary citation

Munzone, A.,El Kerdi, B.,Fanuel, M.,Rogniaux, H.,Ropartz, D.,Reglier, M.,Royant, A.,Simaan, A.J.,Decroos, C.
Characterization of a bacterial copper-dependent lytic polysaccharide monooxygenase with an unusual second coordination sphere.
Febs J., 287:3298-3314, 2020

PubMed Abstract: Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes involved in the degradation of recalcitrant polysaccharides such as cellulose or chitin. LPMOs act in synergy with glycoside hydrolases such as cellulases and chitinases by oxidatively cleaving a number of glycosidic bonds at the surface of their crystalline substrate(s). Besides their role in biomass degradation, some bacterial LPMOs have been found to be virulence factors in some human and insect pathogens. Photorhabdus luminescens is a nematode symbiont bacterium that is pathogenic to a wide range of insects. A single gene encoding a LPMO is found in its genome. In this work, we report the characterization of this LPMO, referred to as PlAA10. Surprisingly, PlAA10 lacks the conserved alanine residue (substituted by an isoleucine) found in the second coordination sphere of the copper-active site in bacterial LPMOs. PlAA10 was found to be catalytically active on both α- and β-chitin, and exhibits a C1-oxidation regiospecificity, similarly to other chitin-active LPMOs. The 1.6 Å X-ray crystal structure confirmed that PlAA10 adopts the canonical immunoglobulin-like fold typical for LPMOs. The geometry of the copper-active site is not affected by the nearby isoleucine, as also supported by electron paramagnetic resonance. Nevertheless, the bulkier side chain of isoleucine protrudes from the substrate-binding surface. A bioinformatic study on putative bacterial LPMOs unveiled that they exhibit some variability at the conserved active-site alanine position with a substitution in about 15% of all sequences analyzed. DATABASE: Structural data (atomic coordinates and structure factors) reported for PlAA10 are available in the Protein Data Bank under accession number 6T5Z. ENZYMES: PlAA10, EC1.14.99.53.

PubMed: 31903721
DOI: 10.1111/febs.15203

Experimental method

X-RAY DIFFRACTION (1.6000030918 Å)