9LYZ|pdb_00009lyz
X-RAY CRYSTALLOGRAPHY OF THE BINDING OF THE BACTERIAL CELL WALL TRISACCHARIDE NAM-NAG-NAM TO LYSOZYME
- PDB DOI: https://doi.org/10.2210/pdb9LYZ/pdb
- Classification: HYDROLASE (O-GLYCOSYL)
- Organism(s): Gallus gallus
- Mutation(s): No
- Deposited: 1979-12-06 Released: 1980-02-27
- Deposition Author(s): Kelly, J.A.,James, M.N.G.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Work: 0.230 (Depositor)
wwPDB Validation 3D Report Full Report
Download MendeleyX-ray crystallography of the binding of the bacterial cell wall trisaccharide NAM-NAG-NAM to lysozyme.
Kelly, J.A., Sielecki, A.R., Sykes, B.D., James, M.N., Phillips, D.C.(1979) Nature 282: 875-878
- PubMed: 514367 Search on PubMed
- DOI: https://doi.org/10.1038/282875a0
- Primary Citation of Related Structures:
9LYZ - PubMed Abstract:
Hen egg white lysozyme was the first enzyme whose structure was determined by X-ray crystallography. The proposed mechanism based on this structure involves the distortion of the saccharide residue (2-acetamido-2-deoxy-D-muramic acid, NAM) in the natural substrate (an alternating beta (1 leads to 4) linked oligomer of 2-acetamido-2-deoxy-D-glucose (NAG) and NAM residues) bound to site D in the binding cleft. The importance of substrate distortion has prompted numerous enzymatic, chemical, theoretical, and physical studies, but there is little direct crystallographic evidence on the conformation of a NAM residue bound at site D. We now present the X-ray structure of the non-hydrolysed trisaccharide NAM-NAG-NAM bound in subsites B, C, D. Our interpretation of the 2.5-A resolution difference map does not involve distortion of this residue in site D. Comparison with the structure of the delta-lactone derived from tetra N-acetylchitotetraose (NAG)3NAL) bound to lysozyme suggests we may be looking at a Michaelis complex.
Explore in 3D: Structure |Sequence Annotations |Validation Report
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Monomer - A1
Find Similar Assemblies
Biological assembly 1 assigned by authors.
Macromolecule Content
- Total Structure Weight: 15.1 kDa
- Atom Count: 1,155
- Modelled Residue Count: 129
- Deposited Residue Count: 129
- Unique protein chains: 1
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| HEN EGG WHITE LYSOZYME | 129 | Gallus gallus | Mutation(s): 0 EC: 3.2.1.17 |  | |
UniProt | |||||
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00698 | ||||
Sequence AnnotationsExpand | |||||
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Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Work: 0.230 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 78.97 | α = 90 |
| b = 78.97 | β = 90 |
| c = 38.25 | γ = 90 |
Deposition Data
- Released Date: 1980-02-27 Deposition Author(s): Kelly, J.A.,James, M.N.G.
Revision History (Full details and data files)
- Version 1.0: 1980-02-27
Type: Initial release - Version 1.1: 2011-06-03
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2011-07-27
Changes: Non-polymer description, Other - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary - Version 2.1: 2024-10-23
Changes: Data collection, Database references, Structure summary
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.