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7DRQ

Crystal structure of polysaccharide lyase Uly1

Summary for 7DRQ
Entry DOI10.2210/pdb7drq/pdb
DescriptorUly1, CALCIUM ION (3 entities in total)
Functional Keywordsulvan lyase, polysaccharide lyase family 24, marine bacterium, lyase
Biological sourceCatenovulum maritimum
Total number of polymer chains2
Total formula weight115010.03
Authors
Chen, X.L.,Cao, H.Y.,Xu, F.,Dong, F. (deposition date: 2020-12-29, release date: 2021-03-31, Last modification date: 2024-11-20)
Primary citationXu, F.,Dong, F.,Sun, X.H.,Cao, H.Y.,Fu, H.H.,Li, C.Y.,Zhang, X.Y.,McMinn, A.,Zhang, Y.Z.,Wang, P.,Chen, X.L.
Mechanistic Insights into Substrate Recognition and Catalysis of a New Ulvan Lyase of Polysaccharide Lyase Family 24.
Appl.Environ.Microbiol., 87:e0041221-e0041221, 2021
Cited by
PubMed Abstract: Ulvan is an important marine polysaccharide. Bacterial ulvan lyases play important roles in ulvan degradation and marine carbon cycling. Until now, only a small number of ulvan lyases have been characterized. Here, a new ulvan lyase, Uly1, belonging to polysaccharide lyase family 24 (PL24) from the marine bacterium Catenovulum maritimum, is characterized. The optimal temperature and pH for Uly1 to degrade ulvan are 40°C and pH 9.0, respectively. Uly1 degrades ulvan polysaccharides in the endolytic manner, mainly producing ΔRha3S, consisting of an unsaturated 4-deoxy-l--hex-4-enopyranosiduronic acid and a 3-O-sulfated α-l-rhamnose. The structure of Uly1 was resolved at a 2.10-Å resolution. Uly1 adopts a seven-bladed β-propeller architecture. Structural and site-directed mutagenesis analyses indicate that four highly conserved residues, H128, H149, Y223, and R239, are essential for catalysis. H128 functions as both the catalytic acid and base, H149 and R239 function as the neutralizers, and Y223 plays a supporting role in catalysis. Structural comparison and sequence alignment suggest that Uly1 and many other PL24 enzymes may directly bind the substrate near the catalytic residues for catalysis, different from the PL24 ulvan lyase LOR_107, which adopts a two-stage substrate binding process. This study provides new insights into ulvan lyases and ulvan degradation. Ulvan is a major cell wall component of green algae of the genus Many marine heterotrophic bacteria can produce extracellular ulvan lyases to degrade ulvan for a carbon nutrient. In addition, ulvan has a range of physiological bioactivities based on its specific chemical structure. Ulvan lyase thus plays an important role in marine carbon cycling and has great potential in biotechnological applications. However, only a small number of ulvan lyases have been characterized over the past 10 years. Here, based on biochemical and structural analyses, a new ulvan lyase of polysaccharide lyase family 24 is characterized, and its substrate recognition and catalytic mechanisms are revealed. Moreover, a new substrate binding process adopted by PL24 ulvan lyases is proposed. This study offers a better understanding of bacterial ulvan lyases and is helpful for studying the application potentials of ulvan lyases.
PubMed: 33771786
DOI: 10.1128/AEM.00412-21
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.79 Å)
Structure validation

239149

数据于2025-07-23公开中

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