3ubp
From Proteopedia
(New page: 200px<br /><applet load="3ubp" size="450" color="white" frame="true" align="right" spinBox="true" caption="3ubp, resolution 2.0Å" /> '''DIAMIDOPHOSPHATE INHI...) |
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| - | [[Image:3ubp.jpg|left|200px]]<br /><applet load="3ubp" size=" | + | [[Image:3ubp.jpg|left|200px]]<br /><applet load="3ubp" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="3ubp, resolution 2.0Å" /> | caption="3ubp, resolution 2.0Å" /> | ||
'''DIAMIDOPHOSPHATE INHIBITED BACILLUS PASTEURII UREASE'''<br /> | '''DIAMIDOPHOSPHATE INHIBITED BACILLUS PASTEURII UREASE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | BACKGROUND: Urease catalyzes the hydrolysis of urea, the final step of | + | BACKGROUND: Urease catalyzes the hydrolysis of urea, the final step of organic nitrogen mineralization, using a bimetallic nickel centre. The role of the active site metal ions and amino acid residues has not been elucidated to date. Many pathologies are associated with the activity of ureolytic bacteria, and the efficiency of soil nitrogen fertilization with urea is severely decreased by urease activity. Therefore, the development of urease inhibitors would lead to a reduction of environmental pollution, to enhanced efficiency of nitrogen uptake by plants, and to improved therapeutic strategies for treatment of infections due to ureolytic bacteria. Structure-based design of urease inhibitors would require knowledge of the enzyme mechanism at the molecular level. RESULTS: The structures of native and inhibited urease from Bacillus pasteurii have been determined at a resolution of 2.0 A by synchrotron X-ray cryogenic crystallography. In the native enzyme, the coordination sphere of each of the two nickel ions is completed by a water molecule and a bridging hydroxide. A fourth water molecule completes a tetrahedral cluster of solvent molecules. The enzyme crystallized in the presence of phenylphosphorodiamidate contains the tetrahedral transition-state analogue diamidophosphoric acid, bound to the two nickel ions in an unprecedented mode. Comparison of the native and inhibited structures reveals two distinct conformations of the flap lining the active-site cavity. CONCLUSIONS: The mode of binding of the inhibitor, and a comparison between the native and inhibited urease structures, indicate a novel mechanism for enzymatic urea hydrolysis which reconciles the available structural and biochemical data. |
==About this Structure== | ==About this Structure== | ||
| - | 3UBP 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, ACE and 2PA 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:// | + | 3UBP 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>, <scene name='pdbligand=ACE:'>ACE</scene> and <scene name='pdbligand=2PA:'>2PA</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=3UBP OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Mangani, S.]] | [[Category: Mangani, S.]] | ||
[[Category: Miletti, S.]] | [[Category: Miletti, S.]] | ||
| - | [[Category: Rypniewski, W | + | [[Category: Rypniewski, W R.]] |
| - | [[Category: Wilson, K | + | [[Category: Wilson, K S.]] |
[[Category: 2PA]] | [[Category: 2PA]] | ||
[[Category: ACE]] | [[Category: ACE]] | ||
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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 19:11:39 2008'' |
Revision as of 17:11, 21 February 2008
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DIAMIDOPHOSPHATE INHIBITED BACILLUS PASTEURII UREASE
Overview
BACKGROUND: Urease catalyzes the hydrolysis of urea, the final step of organic nitrogen mineralization, using a bimetallic nickel centre. The role of the active site metal ions and amino acid residues has not been elucidated to date. Many pathologies are associated with the activity of ureolytic bacteria, and the efficiency of soil nitrogen fertilization with urea is severely decreased by urease activity. Therefore, the development of urease inhibitors would lead to a reduction of environmental pollution, to enhanced efficiency of nitrogen uptake by plants, and to improved therapeutic strategies for treatment of infections due to ureolytic bacteria. Structure-based design of urease inhibitors would require knowledge of the enzyme mechanism at the molecular level. RESULTS: The structures of native and inhibited urease from Bacillus pasteurii have been determined at a resolution of 2.0 A by synchrotron X-ray cryogenic crystallography. In the native enzyme, the coordination sphere of each of the two nickel ions is completed by a water molecule and a bridging hydroxide. A fourth water molecule completes a tetrahedral cluster of solvent molecules. The enzyme crystallized in the presence of phenylphosphorodiamidate contains the tetrahedral transition-state analogue diamidophosphoric acid, bound to the two nickel ions in an unprecedented mode. Comparison of the native and inhibited structures reveals two distinct conformations of the flap lining the active-site cavity. CONCLUSIONS: The mode of binding of the inhibitor, and a comparison between the native and inhibited urease structures, indicate a novel mechanism for enzymatic urea hydrolysis which reconciles the available structural and biochemical data.
About this Structure
3UBP 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.
Reference
A new proposal for urease mechanism based on the crystal structures of the native and inhibited enzyme from Bacillus pasteurii: why urea hydrolysis costs two nickels., Benini S, Rypniewski WR, Wilson KS, Miletti S, Ciurli S, Mangani S, Structure. 1999 Feb 15;7(2):205-16. PMID:10368287
Page seeded by OCA on Thu Feb 21 19:11:39 2008
Categories: Protein complex | Sporosarcina pasteurii | Urease | Benini, S. | Ciurli, S. | Mangani, S. | Miletti, S. | Rypniewski, W R. | Wilson, K S. | 2PA | ACE | NI | Bacillus pasteurii | Diamidophosphate | Metalloenzyme | Nickel
