8acn
From Proteopedia
(New page: 200px<br /><applet load="8acn" size="450" color="white" frame="true" align="right" spinBox="true" caption="8acn, resolution 2.0Å" /> '''CRYSTAL STRUCTURES OF...) |
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| - | [[Image:8acn.gif|left|200px]]<br /><applet load="8acn" size=" | + | [[Image:8acn.gif|left|200px]]<br /><applet load="8acn" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="8acn, resolution 2.0Å" /> | caption="8acn, resolution 2.0Å" /> | ||
'''CRYSTAL STRUCTURES OF ACONITASE WITH ISOCITRATE AND NITROISOCITRATE BOUND'''<br /> | '''CRYSTAL STRUCTURES OF ACONITASE WITH ISOCITRATE AND NITROISOCITRATE BOUND'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structures of mitochondrial aconitase with isocitrate and | + | The crystal structures of mitochondrial aconitase with isocitrate and nitroisocitrate bound have been solved and refined to R factors of 0.179 and 0.161, respectively, for all observed data in the range 8.0-2.1 A. Porcine heart enzyme was used for determining the structure with isocitrate bound. The presence of isocitrate in the crystals was corroborated by Mossbauer spectroscopy. Bovine heart enzyme was used for determining the structure with the reaction intermediate analogue nitroisocitrate bound. The inhibitor binds to the enzyme in a manner virtually identical to that of isocitrate. Both compounds bind to the unique Fe atom of the [4Fe-4S] cluster via a hydroxyl oxygen and one carboxyl oxygen. A H2O molecule is also bound, making Fe six-coordinate. The unique Fe is pulled away approximately 0.2 A from the corner of the cubane compared to the position it would occupy in a symmetrically ligated [4Fe-4S] cluster. At least 23 residues from all four domains of aconitase contribute to the active site. These residues participate in substrate recognition (Arg447, Arg452, Arg580, Arg644, Gln72, Ser166, Ser643), cluster ligation and interaction (Cys358, Cys421, Cys424, Asn258, Asn446), and hydrogen bonds supporting active site side chains (Ala74, Asp568, Ser571, Thr567). Residues implicated in catalysis are Ser642 and three histidine-carboxylate pairs (Asp100-His101, Asp165-His147, Glu262-His167). The base necessary for proton abstraction from C beta of isocitrate appears to be Ser642; the O gamma atom is proximal to the calculated hydrogen position, while the environment of O gamma suggests stabilization of an alkoxide (an oxyanion hole formed by the amide and side chain of Arg644). The histidine-carboxylate pairs appear to be required for proton transfer reactions involving two oxygens bound to Fe, one derived from solvent (bound H2O) and one derived from substrate hydroxyl. Each oxygen is in contact with a histidine, and both are in contact with the side chain of Asp165, which bridges the two sites on the six-coordinate Fe. |
==About this Structure== | ==About this Structure== | ||
| - | 8ACN 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 SF4 and NIC 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:// | + | 8ACN 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=SF4:'>SF4</scene> and <scene name='pdbligand=NIC:'>NIC</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=8ACN 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: NIC]] | [[Category: NIC]] | ||
[[Category: SF4]] | [[Category: SF4]] | ||
[[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 19:17:45 2008'' |
Revision as of 17:17, 21 February 2008
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CRYSTAL STRUCTURES OF ACONITASE WITH ISOCITRATE AND NITROISOCITRATE BOUND
Overview
The crystal structures of mitochondrial aconitase with isocitrate and nitroisocitrate bound have been solved and refined to R factors of 0.179 and 0.161, respectively, for all observed data in the range 8.0-2.1 A. Porcine heart enzyme was used for determining the structure with isocitrate bound. The presence of isocitrate in the crystals was corroborated by Mossbauer spectroscopy. Bovine heart enzyme was used for determining the structure with the reaction intermediate analogue nitroisocitrate bound. The inhibitor binds to the enzyme in a manner virtually identical to that of isocitrate. Both compounds bind to the unique Fe atom of the [4Fe-4S] cluster via a hydroxyl oxygen and one carboxyl oxygen. A H2O molecule is also bound, making Fe six-coordinate. The unique Fe is pulled away approximately 0.2 A from the corner of the cubane compared to the position it would occupy in a symmetrically ligated [4Fe-4S] cluster. At least 23 residues from all four domains of aconitase contribute to the active site. These residues participate in substrate recognition (Arg447, Arg452, Arg580, Arg644, Gln72, Ser166, Ser643), cluster ligation and interaction (Cys358, Cys421, Cys424, Asn258, Asn446), and hydrogen bonds supporting active site side chains (Ala74, Asp568, Ser571, Thr567). Residues implicated in catalysis are Ser642 and three histidine-carboxylate pairs (Asp100-His101, Asp165-His147, Glu262-His167). The base necessary for proton abstraction from C beta of isocitrate appears to be Ser642; the O gamma atom is proximal to the calculated hydrogen position, while the environment of O gamma suggests stabilization of an alkoxide (an oxyanion hole formed by the amide and side chain of Arg644). The histidine-carboxylate pairs appear to be required for proton transfer reactions involving two oxygens bound to Fe, one derived from solvent (bound H2O) and one derived from substrate hydroxyl. Each oxygen is in contact with a histidine, and both are in contact with the side chain of Asp165, which bridges the two sites on the six-coordinate Fe.
About this Structure
8ACN 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 isocitrate and nitroisocitrate bound., Lauble H, Kennedy MC, Beinert H, Stout CD, Biochemistry. 1992 Mar 17;31(10):2735-48. PMID:1547214
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