PDBsum entry 1skb

Hydrolase

PDB id: 1skb

Contents

Protein chain

435 a.a. *

Ligands

NAG ×6

Waters ×746

* Residue conservation analysis

PDB id:

1skb

Name:

Hydrolase

Title:

Crystallographic snapshots of aspergillus fumigatus phytase revealing its enzymatic dynamics

Structure:

3-phytase a. Chain: a. Synonym: myo-inositol-hexaphosphate 3- phosphohydrolase a, 3 phytase a, myo-inositol hexakisphosphate phosphohydrolase a. Engineered: yes

Source:

Aspergillus fumigatus. Organism_taxid: 5085. Gene: phya. Expressed in: pichia pastoris. Expression_system_taxid: 4922

Resolution:

1.58Å R-factor: 0.156 R-free: 0.182

Authors:

Q.Liu,Q.Huang,X.G.Lei,Q.Hao

Key ref:

Q.Liu et al. (2004). Crystallographic snapshots of Aspergillus fumigatus phytase, revealing its enzymatic dynamics. Structure, 12, 1575-1583. PubMed id: 15341723 DOI: 10.1016/j.str.2004.06.015

Date:

04-Mar-04 Release date: 28-Sep-04

Protein chain

O00092  (PHYA_ASPFU) -  Phytase A from Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)

Seq: 465 a.a.

Struc: 435 a.a.

Enzyme reactions

• Enzyme class 1: E.C.3.1.3.- - ?????
• Enzyme class 2: E.C.3.1.3.8 - 3-phytase.
• Reaction: 1D-myo-inositol hexakisphosphate + H2O = 1D-myo-inositol 1,2,4,5,6- pentakisphosphate + phosphate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.str.2004.06.015

Structure 12:1575-1583 (2004)

PubMed id: 15341723

Crystallographic snapshots of Aspergillus fumigatus phytase, revealing its enzymatic dynamics.

Q.Liu, Q.Huang, X.G.Lei, Q.Hao.

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.

Selected figure(s)

Figure 7.
Figure 7. The Release Pathway of Phosphate IonsPO4 501 is the phosphate near the catalytic residue and PO4 502 is the phosphate with hydrogen bonding to five water molecules. This figure was prepared with Ligplot (Wallace et al., 1995).

The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 1575-1583) copyright 2004.

Figure was selected by an automated process.