1ie7: Difference between revisions
New page: left|200px<br /><applet load="1ie7" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ie7, resolution 1.85Å" /> '''PHOSPHATE INHIBITED ... |
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[[Image:1ie7.gif|left|200px]]<br /><applet load="1ie7" size=" | [[Image:1ie7.gif|left|200px]]<br /><applet load="1ie7" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1ie7, resolution 1.85Å" /> | caption="1ie7, resolution 1.85Å" /> | ||
'''PHOSPHATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE'''<br /> | '''PHOSPHATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE'''<br /> | ||
==Overview== | ==Overview== | ||
The structure of Bacillus pasteurii urease (BPU) inhibited with phosphate | 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. | ||
==About this Structure== | ==About this Structure== | ||
1IE7 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Sporosarcina_pasteurii Sporosarcina pasteurii] with NI and PO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Urease Urease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] Full crystallographic information is available from [http:// | 1IE7 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Sporosarcina_pasteurii Sporosarcina pasteurii] with <scene name='pdbligand=NI:'>NI</scene> and <scene name='pdbligand=PO4:'>PO4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Urease Urease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IE7 OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Ciurli, S.]] | [[Category: Ciurli, S.]] | ||
[[Category: Mangani, S.]] | [[Category: Mangani, S.]] | ||
[[Category: Rypniewski, W | [[Category: Rypniewski, W R.]] | ||
[[Category: Wilson, K | [[Category: Wilson, K S.]] | ||
[[Category: NI]] | [[Category: NI]] | ||
[[Category: PO4]] | [[Category: PO4]] | ||
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[[Category: urease]] | [[Category: urease]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:10:59 2008'' | ||
Revision as of 14:11, 21 February 2008
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PHOSPHATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE
OverviewOverview
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.
About this StructureAbout this Structure
1IE7 is a Protein complex structure of sequences from Sporosarcina pasteurii with and as ligands. Active as Urease, with EC number 3.5.1.5 Full crystallographic information is available from OCA.
ReferenceReference
Structure-based rationalization of urease inhibition by phosphate: novel insights into the enzyme mechanism., Benini S, Rypniewski WR, Wilson KS, Ciurli S, Mangani S, J Biol Inorg Chem. 2001 Oct;6(8):778-90. PMID:11713685
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