6IDN

Crystal structure of ICChI chitinase from ipomoea carnea

Summary for 6IDN

• Entry DOI: 10.2210/pdb6idn/pdb
• Descriptor: ICChI, a glycosylated chitinase, alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose, beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: chitinase, glycosylation, tim barrel, ipomoea carnea, plant protein
• Biological source: Ipomoea carnea
• Total number of polymer chains: 1
• Total formula weight: 32247.06

Authors

Kumar, S.,Kumar, A.,Patel, A.K. (deposition date: 2018-09-10, release date: 2018-11-21, Last modification date: 2023-11-22)

Primary citation

Kumar, S.,Kumar, A.,Patel, A.K.
TIM barrel fold and glycan moieties in the structure of ICChI, a protein with chitinase and lysozyme activity.
Phytochemistry, 170:112221-112221, 2020

PubMed Abstract: The ICChI is a 35-kDa, glycosylated protein isolated from the latex of the weed Ipomoea carnea. It displays chitinase and lysozyme activity, which could be important for the defense against pathogenic fungi, insects and bacteria. The ICChI enzyme was crystallized, and a diffraction data set was collected from a single crystal to 1.42 Å resolution. The crystals belong to the primitive tetragonal space group P422, with unit-cell parameters a = b = 57.9, c = 172.0 Å, and α = β = γ = 90°. The structure was elucidated by molecular replacement method using a mixed model of three homologous structures from the N-terminal sequence of ICChI. The refined model consists of 272 amino acid residues and has a R of 18.93% and R of 22.42%. The protein consists of a single globular domain with a (α/β) triosephosphate isomerase barrel fold. Three of the consensus sites for N-glycosylation viz., Asn, Asn, and Asn containing carbohydrate moieties N-Acetylglucosamine (NAG), mannose, fucose, and xylose. The putative catalytic residues are Asp, Glu, and Tyr. The crystal structure may provide fundamental information of GH18 family chitinases.

PubMed: 31790908
DOI: 10.1016/j.phytochem.2019.112221

Experimental method

X-RAY DIFFRACTION (1.5 Å)