7EIR

Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 6S

Summary for 7EIR

• Entry DOI: 10.2210/pdb7eir/pdb
• Descriptor: Chondroitin sulfate ABC endolyase, 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-6-O-sulfo-beta-D-galactopyranose, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: polysaccharide lyase family 8, carbohydrate binding, lyase
• Biological source: Proteus vulgaris
• Total number of polymer chains: 1
• Total formula weight: 116251.55

Authors

Takashima, M.,Miyanaga, A.,Eguchi, T. (deposition date: 2021-03-31, release date: 2021-08-25, Last modification date: 2023-11-29)

Primary citation

Takashima, M.,Watanabe, I.,Miyanaga, A.,Eguchi, T.
Substrate specificity of Chondroitinase ABC I based on analyses of biochemical reactions and crystal structures in complex with disaccharides.
Glycobiology, 31:1571-1581, 2021

PubMed Abstract: Chondroitinase ABC I (cABC-I) is the enzyme which cleaves the β-1,4 glycosidic linkage of chondroitin sulfate (CS) by β-elimination. To elucidate more accurately the substrate specificity of cABC-I, we evaluated the kinetic parameters of cABC-I and its reactivity with CS isomers displaying less structural heterogeneity as substrates, e.g., approximately 90 percent of disaccharide units in Chondroitin sulfate A (CSA) or Chondroitin sulfate C (CSC) is D-glucuronic acid and 4-O-sulfated N-acetyl galactosamine (GalNAc) (A-unit) or D-glucuronic acid and 6-O-sulfated GalNAc (C-unit), respectively. cABC-I showed the highest reactivity to CSA and CSC among all CS isomers, and the kcat/Km of cABC-I was higher for CSA than for CSC. Next, we determined the crystal structures of cABC-I in complex with CS disaccharides, and analyzed the crystallographic data in combination with molecular docking data. Arg500 interacts with 4-O-sulfated and 6-O-sulfated GalNAc residues. The distance between Arg500 and the 4-O-sulfate group was 0.8 Å shorter than that between Arg500 and the 6-O-sulfated group. Moreover, it is likely that the 6-O-sulfated group is electrostatically repulsed by the nearby Asp490. Thus, we demonstrated that cABC-I has the highest affinity for the CSA richest in 4-O-sulfated GalNAc residues among all CS isomers. Recently, cABC-I was used to treat lumbar disc herniation. The results provide useful information to understand the mechanism of the pharmacological action of cABC-I.

PubMed: 34392362
DOI: 10.1093/glycob/cwab086

Experimental method

X-RAY DIFFRACTION (1.92 Å)