1SKB

Crystallographic snapshots of Aspergillus fumigatus phytase revealing its enzymatic dynamics

Summary for 1SKB

• Entry DOI: 10.2210/pdb1skb/pdb
• Related: 1QWO 1SK8 1SK9 1SKA
• Descriptor: 3-phytase A, 2-acetamido-2-deoxy-beta-D-glucopyranose (3 entities in total)
• Functional Keywords: small alpha domain, big alpha/beta domain, catalytic sites, water structures, catalytic dynamics, product release pathway, hydrolase
• Biological source: Aspergillus fumigatus
• Cellular location: Secreted: O00092
• Total number of polymer chains: 1
• Total formula weight: 49650.52

Authors

Liu, Q.,Huang, Q.,Lei, X.G.,Hao, Q. (deposition date: 2004-03-04, release date: 2004-09-28, Last modification date: 2024-11-06)

Primary citation

Liu, Q.,Huang, Q.,Lei, X.G.,Hao, Q.
Crystallographic Snapshots of Aspergillus fumigatus Phytase, Revealing Its Enzymatic Dynamics
Structure, 12:1575-1583, 2004

PubMed Abstract: Understanding of the atomic movements involved in an enzymatic reaction needs structural information on the active and inactive native enzyme molecules and on the enzyme-substrate, enzyme-intermediate, and enzyme-product(s) complexes. By using the X-ray crystallographic method, four crystal structures of Aspergillus fumigatus phytase were obtained at resolution higher than 1.7 A. The pH-dependent catalytic activity of A. fumigatus phytase was linked to three water molecules that may prevent the substrate from binding and thus block nucleophilic attack of the catalytic imidazole nitrogen. Comparison of various structures also identified the water molecule that attacks the phosphamide bond during the hydrolysis process, and established the hydrolysis pathway of the intermediate. Additionally, two reaction product phosphates were observed at the active site, suggesting a possible product release pathway after hydrolysis of the intermediate. These results can help explain the catalytic mechanism throughout the whole acid phosphatase family, as all key residues are conserved.

PubMed: 15341723
DOI: 10.1016/j.str.2004.06.015

Experimental method

X-RAY DIFFRACTION (1.58 Å)