7acn | pdb_00007acn

CRYSTAL STRUCTURES OF ACONITASE WITH ISOCITRATE AND NITROISOCITRATE BOUND

spinqualitylabelsall models 7acn, resolution 2.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7acn is a 1 chain structure with sequence from Pig. The May 2007 RCSB PDB Molecule of the Month feature on Aconitase and Iron Regulatory Protein 1 by David S. Goodsell is 10.2210/rcsb_pdb/mom_2007_5. The October 2012 RCSB PDB Molecule of the Month feature on Citric Acid Cycle by David Goodsell is 10.2210/rcsb_pdb/mom_2012_10. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ICT, SF4 NonStd Res: PCA Activity: Aconitate hydratase, with EC number 4.2.1.3 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [ACON_PIG] Catalyzes the isomerization of citrate to isocitrate via cis-aconitate. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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