6BYT

Complex structure of LOR107 mutant (R320) with tetrasaccharide substrate

Summary for 6BYT

• Entry DOI: 10.2210/pdb6byt/pdb
• Descriptor: Short ulvan lyase, 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-3-O-sulfo-alpha-L-rhamnopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-3-O-sulfo-alpha-L-rhamnopyranose, CALCIUM ION, ... (6 entities in total)
• Functional Keywords: complex of lor107 (r320), lyase
• Biological source: Alteromonas sp. LOR
• Total number of polymer chains: 2
• Total formula weight: 117752.59

Authors

Ulaganathan, T.S.,Cygler, M. (deposition date: 2017-12-21, release date: 2018-02-07, Last modification date: 2024-03-13)

Primary citation

Ulaganathan, T.,Helbert, W.,Kopel, M.,Banin, E.,Cygler, M.
Structure-function analyses of a PL24 family ulvan lyase reveal key features and suggest its catalytic mechanism.
J. Biol. Chem., 293:4026-4036, 2018

PubMed Abstract: Ulvan is a major cell wall component of green algae of the genus , and some marine bacteria encode enzymes that can degrade this polysaccharide. The first ulvan-degrading lyases have been recently characterized, and several putative ulvan lyases have been recombinantly expressed, confirmed as ulvan lyases, and partially characterized. Two families of ulvan-degrading lyases, PL24 and PL25, have recently been established. The PL24 lyase LOR_107 from the bacterial sp. strain LOR degrades ulvan endolytically, cleaving the bond at the C4 of a glucuronic acid. However, the mechanism and LOR_107 structural features involved are unknown. We present here the crystal structure of LOR_107, representing the first PL24 family structure. We found that LOR_107 adopts a seven-bladed β-propeller fold with a deep canyon on one side of the protein. Comparative sequence analysis revealed a cluster of conserved residues within this canyon, and site-directed mutagenesis disclosed several residues essential for catalysis. We also found that LOR_107 uses the His/Tyr catalytic mechanism, common to several PL families. We captured a tetrasaccharide substrate in the structures of two inactive mutants, which indicated a two-step binding event, with the first substrate interaction near the top of the canyon coordinated by Arg, followed by sliding of the substrate into the canyon toward the active-site residues. Surprisingly, the LOR_107 structure was very similar to that of the PL25 family PLSV_3936, despite only ∼14% sequence identity between the two enzymes. On the basis of our structural and mutational analyses, we propose a catalytic mechanism for LOR_107 that differs from the typical His/Tyr mechanism.

PubMed: 29382716
DOI: 10.1074/jbc.RA117.001642

Experimental method

X-RAY DIFFRACTION (2.2 Å)