1nit
From Proteopedia
(New page: 200px<br /><applet load="1nit" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nit, resolution 2.05Å" /> '''CRYSTAL STRUCTURE OF...) |
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| - | [[Image:1nit.gif|left|200px]]<br /><applet load="1nit" size=" | + | [[Image:1nit.gif|left|200px]]<br /><applet load="1nit" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1nit, resolution 2.05Å" /> | caption="1nit, resolution 2.05Å" /> | ||
'''CRYSTAL STRUCTURE OF ACONITASE WITH TRANS-ACONITATE AND NITROCITRATE BOUND'''<br /> | '''CRYSTAL STRUCTURE OF ACONITASE WITH TRANS-ACONITATE AND NITROCITRATE BOUND'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Crystal structures of mitochondrial aconitase with the inhibitors | + | Crystal structures of mitochondrial aconitase with the inhibitors trans-aconitate and nitrocitrate bound to the [4Fe-4S] cluster have been solved and refined at 2.05 A resolution with R-factors of 0.168 and 0.172, respectively. Crystallization of aconitase with the substrates citrate and cis-aconitate has not been possible because the enzyme turns over and selects enzyme with isocitrate bound into the crystal lattice. Therefore we have analyzed crystal structures of the enzyme complexed with inhibitor analogs of these two substrates. The structure with nitrocitrate bound provides a model for citrate binding. The structure with trans-aconitate bound provides a model for cis-aconitate binding in two ways: Fe4 of the [4Fe-4S] cluster is five-coordinate and the carbon at the C beta position is trigonal. These results allow the model for the reaction mechanism to be extended to all three natural substrates of aconitase. The results support a model in which citrate and isocitrate form similar chelate structures related by 180 degrees rotation about the C alpha-C beta bond while the intermediate cis-aconitate binds in either of two ways (citrate mode or isocitrate mode). In both inhibitor complexes a H2O molecule is also bound to Fe4. In the structure with nitrocitrate bound, partial occupancy of sulfate in the active site is observed accompanied by hydroxyl binding to Fe4. Comparison of the structures with isocitrate, trans-aconitate, nitrocitrate and sulfate bound reveals preferred orientations for the three types of oxygens ligated to Fe4 (carboxyl, hydroxyl and H2O) supporting the proposed roles for His101, Asp165 and His167 in the catalytic mechanism. |
==About this Structure== | ==About this Structure== | ||
| - | 1NIT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with SO4 and SF4 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Aconitate_hydratase Aconitate hydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.3 4.2.1.3] Full crystallographic information is available from [http:// | + | 1NIT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=SF4:'>SF4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Aconitate_hydratase Aconitate hydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.3 4.2.1.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIT OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Beinert, H.]] | [[Category: Beinert, H.]] | ||
| - | [[Category: Kennedy, M | + | [[Category: Kennedy, M C.]] |
[[Category: Lauble, H.]] | [[Category: Lauble, H.]] | ||
| - | [[Category: Stout, C | + | [[Category: Stout, C D.]] |
[[Category: SF4]] | [[Category: SF4]] | ||
[[Category: SO4]] | [[Category: SO4]] | ||
[[Category: lyase(carbon-oxygen)]] | [[Category: lyase(carbon-oxygen)]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:06:34 2008'' |
Revision as of 12:06, 21 February 2008
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CRYSTAL STRUCTURE OF ACONITASE WITH TRANS-ACONITATE AND NITROCITRATE BOUND
Overview
Crystal structures of mitochondrial aconitase with the inhibitors trans-aconitate and nitrocitrate bound to the [4Fe-4S] cluster have been solved and refined at 2.05 A resolution with R-factors of 0.168 and 0.172, respectively. Crystallization of aconitase with the substrates citrate and cis-aconitate has not been possible because the enzyme turns over and selects enzyme with isocitrate bound into the crystal lattice. Therefore we have analyzed crystal structures of the enzyme complexed with inhibitor analogs of these two substrates. The structure with nitrocitrate bound provides a model for citrate binding. The structure with trans-aconitate bound provides a model for cis-aconitate binding in two ways: Fe4 of the [4Fe-4S] cluster is five-coordinate and the carbon at the C beta position is trigonal. These results allow the model for the reaction mechanism to be extended to all three natural substrates of aconitase. The results support a model in which citrate and isocitrate form similar chelate structures related by 180 degrees rotation about the C alpha-C beta bond while the intermediate cis-aconitate binds in either of two ways (citrate mode or isocitrate mode). In both inhibitor complexes a H2O molecule is also bound to Fe4. In the structure with nitrocitrate bound, partial occupancy of sulfate in the active site is observed accompanied by hydroxyl binding to Fe4. Comparison of the structures with isocitrate, trans-aconitate, nitrocitrate and sulfate bound reveals preferred orientations for the three types of oxygens ligated to Fe4 (carboxyl, hydroxyl and H2O) supporting the proposed roles for His101, Asp165 and His167 in the catalytic mechanism.
About this Structure
1NIT is a Single protein structure of sequence from Bos taurus with and as ligands. Active as Aconitate hydratase, with EC number 4.2.1.3 Full crystallographic information is available from OCA.
Reference
Crystal structures of aconitase with trans-aconitate and nitrocitrate bound., Lauble H, Kennedy MC, Beinert H, Stout CD, J Mol Biol. 1994 Apr 8;237(4):437-51. PMID:8151704
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