1IE7
PHOSPHATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE
Summary for 1IE7
| Entry DOI | 10.2210/pdb1ie7/pdb |
| Related | 1ubp 2ubp 3ubp 4ubp |
| Descriptor | UREASE GAMMA SUBUNIT, UREASE BETA SUBUNIT, UREASE ALPHA SUBUNIT, ... (6 entities in total) |
| Functional Keywords | urease, bacillus pasteurii, nickel, metalloenzyme, hydrolase |
| Biological source | Sporosarcina pasteurii More |
| Cellular location | Cytoplasm (By similarity): P41022 P41021 P41020 |
| Total number of polymer chains | 3 |
| Total formula weight | 87025.63 |
| Authors | Benini, S.,Rypniewski, W.R.,Wilson, K.S.,Ciurli, S.,Mangani, S. (deposition date: 2001-04-09, release date: 2001-04-25, Last modification date: 2023-11-15) |
| Primary citation | Benini, S.,Rypniewski, W.R.,Wilson, K.S.,Ciurli, S.,Mangani, S. Structure-based rationalization of urease inhibition by phosphate: novel insights into the enzyme mechanism. J.Biol.Inorg.Chem., 6:778-790, 2001 Cited by PubMed Abstract: The structure of Bacillus pasteurii urease (BPU) inhibited with phosphate was solved and refined using synchrotron X-ray diffraction data from a vitrified crystal (1.85 A resolution, 99.3% completeness, data redundancy 4.6, R-factor 17.3%, PDB code 6UBP). A distance of 3.5 A separates the two Ni ions in the active site. The binding mode of the inhibitor involves the formation of four coordination bonds with the two Ni ions: one phosphate oxygen atom symmetrically bridges the two metal ions (1.9-2.0 A), while two of the remaining phosphate oxygen atoms bind to the Ni atoms at 2.4 A. The fourth phosphate oxygen is directed into the active site channel. Analysis of the H-bonding network around the bound inhibitor indicates that phosphate is bound as the H2PO4- anion, and that an additional proton is present on the Odelta2 atom of Asp(alpha363), an active site residue involved in Ni coordination through Odelta1. The flexible flap flanking the active site cavity is in the open conformation. Analysis of the complex reveals why phosphate is a relatively weak inhibitor and why sulfate does not bind to the nickels in the active site. The implications of the results for the understanding of the urease catalytic mechanism are reviewed. A novel alternative for the proton donor is presented. PubMed: 11713685DOI: 10.1007/s007750100254 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.85 Å) |
Structure validation
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