3AB6

Crystal structure of NAG3 bound lysozyme from Meretrix lusoria

Summary for 3AB6

• Entry DOI: 10.2210/pdb3ab6/pdb
• Related PRD ID: PRD_900017
• Descriptor: Lysozyme, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose (3 entities in total)
• Functional Keywords: lysozyme, meretrix lusoria, antibiotic, antimicrobial, bacteriolytic enzyme, glycosidase, hydrolase, secreted
• Biological source: Meretrix lusoria (Hard clam)
• Cellular location: Secreted : P86383
• Total number of polymer chains: 1
• Total formula weight: 14012.11

Authors

Yoneda, K.,Kuwano, Y.,Araki, T. (deposition date: 2009-12-01, release date: 2010-12-01, Last modification date: 2024-10-16)

Primary citation

Kuwano, Y.,Yoneda, K.,Kawaguchi, Y.,Araki, T.
The tertiary structure of an i-type lysozyme isolated from the common orient clam (Meretrix lusoria)
Acta Crystallogr.,Sect.F, 69:1202-1206, 2013

PubMed Abstract: To evaluate the structure-function relationships of invertebrate lysozymes, a new invertebrate-type (i-type) lysozyme was isolated from the common orient clam (Meretrix lusoria) and the tertiary structure of this enzyme was determined. Comparison of the tertiary structure of this enzyme with those of chicken and Venerupi philippinarum lysozymes revealed that the location of the side chain of the second catalytic residue, an aspartic acid, and the N-acetylglucosamine trimer bound at subsites A-C were different. Furthermore, the amino acid electrostatically interacting with Asp30 in V. philippinarum lysozyme, Lys108, was substituted by Gly in M. lusoria lysozyme and no other possible amino acid that could contribute to this interaction was found in M. lusoria lysozyme. It therefore seems that the substitutions of the amino acids at the interface of the V. philippinarum lysozyme dimer are likely to change the oligomeric state of the M. lusoria lysozyme.

PubMed: 24192349
DOI: 10.1107/S1744309113028170

Experimental method

X-RAY DIFFRACTION (1.78 Å)