3GXR
The crystal structure of g-type lysozyme from Atlantic cod (Gadus morhua L.) in complex with NAG oligomers sheds new light on substrate binding and the catalytic mechanism. Structure with NAG to 1.7
Summary for 3GXR
| Entry DOI | 10.2210/pdb3gxr/pdb |
| Related | 3GXK |
| Related PRD ID | PRD_900017 |
| Descriptor | Goose-type lysozyme 1, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 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, ... (4 entities in total) |
| Functional Keywords | atlantic cod, fish lysozyme, active site residues, substrate binding sites, surface potential, muramidase activity, immune system, hydrolase |
| Biological source | Gadus morhua (Atlantic cod) |
| Total number of polymer chains | 4 |
| Total formula weight | 86055.62 |
| Authors | Helland, R.,Larsen, R.L.,Finstad, S.,Kyomuhendo, P.,Larsen, A.N. (deposition date: 2009-04-02, release date: 2009-10-20, Last modification date: 2023-11-01) |
| Primary citation | Helland, R.,Larsen, R.L.,Finstad, S.,Kyomuhendo, P.,Larsen, A.N. Crystal structures of g-type lysozyme from Atlantic cod shed new light on substrate binding and the catalytic mechanism. Cell.Mol.Life Sci., 66:2585-2598, 2009 Cited by PubMed Abstract: Crystal structures of Atlantic cod lysozyme have been solved with and without ligand bound in the active site to 1.7 and 1.9 A resolution, respectively. The structures reveal the presence of NAG in the substrate binding sites at both sides of the catalytic Glu73, hence allowing the first crystallographic description of the goose-type (g-type) lysozyme E-G binding sites. In addition, two aspartic acid residues suggested to participate in catalysis (Asp101 and Asp90) were mutated to alanine. Muramidase activity data for two single mutants and one double mutant demonstrates that both residues are involved in catalysis, but Asp101 is the more critical of the two. The structures and activity data suggest that a water molecule is the nucleophile completing the catalytic reaction, and the roles of the aspartic acids are to ensure proper positioning of the catalytic water. PubMed: 19543850DOI: 10.1007/s00018-009-0063-x PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.7 Å) |
Structure validation
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