User:Cameron Evans/Sandbox 1: Difference between revisions
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GluDH is at the threshold of carbon metabolism (GluDH feeds α-ketoglutarate into the tricarboxylic acid cycle) and nitrogen metabolism (the amine product is utilized by other biosynthetic pathways).<ref name="1hwxyz">PMID:11254391</ref>. Due to its prominent position on the threshold between catabolic and anabolic pathways, GluDH is ubiquitously expressed in both complex and simple organisms.<ref name="1hwx">PMID:10425679</ref> | GluDH is at the threshold of carbon metabolism (GluDH feeds α-ketoglutarate into the tricarboxylic acid cycle) and nitrogen metabolism (the amine product is utilized by other biosynthetic pathways).<ref name="1hwxyz">PMID:11254391</ref>. Due to its prominent position on the threshold between catabolic and anabolic pathways, GluDH is ubiquitously expressed in both complex and simple organisms.<ref name="1hwx">PMID:10425679</ref> | ||
In vertebrates | In vertebrates and plants, GluDH is preferentially found in the mitochondria, but also in the cytoplasm. In prokaryotes it is found in the cytosol.<ref>[http://www.brenda-enzymes.org/php/flat_result.php4?ecno=1.4.1.2&organism_list=&Suchword=&UniProtAcc=#LOCALIZATION EC 1.4.1.2] Brenda 2010</ref> | ||
Reductive amination of α-ketoglutarate (α-KG) is the process by which the ketone is converted to an amine via an imine intermediate. The reverse reaction, oxidative deamination, is the conversion of the amine functional group to a ketone. | Reductive amination of α-ketoglutarate (α-KG) is the process by which the ketone is converted to an amine via an imine intermediate. The reverse reaction, oxidative deamination, is the conversion of the amine functional group to a ketone. | ||
In vertebrates the produced ammonia is usually utilized in the urea cycle and in bacteria the ammonia is assimilated to amino acids and amidotransferases.<ref name="Lightfoot_1988">Lightfoot DA, Baron AJ, Wootton JC (1988). "Expression of the Escherichia coli glutamate dehydrogenase gene in the cyanobacterium Synechococcus PCC6301 causes ammonium tolerance". Plant Molecular Biology 11 (3): 335-344. [http://www.springerlink.com/content/w2721u62r8021510/ doi 10.1007/BF00027390]</ref> | |||
Glutamate dehydrogenase shares sequence homology and structural homology to the superfamily of amino acid dehydrogenases, which supports the idea that this superfamily formed by divergent evolution. <ref name="1bgv" /> Because of the homology among all proteins in this superfamily, many dehydrogenases can work on multiple substrates. Nonetheless, GluDH appears to be very specific towards its substrates. | Glutamate dehydrogenase shares sequence homology and structural homology to the superfamily of amino acid dehydrogenases, which supports the idea that this superfamily formed by divergent evolution. <ref name="1bgv" /> Because of the homology among all proteins in this superfamily, many dehydrogenases can work on multiple substrates. Nonetheless, GluDH appears to be very specific towards its substrates. | ||
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In the apo form of csGluDH, K113 (domain I) is hydrogen bound to N373 (domain II) and stabilizes the open structure. On substrate binding, K113 moves to hydrogen bond to the alpha carbonyl of the substrate while maintaining contact with N373. This causes the conformational change which closes the cleft. Based on the crystal structures of csGluDH and previous binding studies with boGluDH, Stillman and Baker, ‘’et al’’ (1993) have proposed the following catalytic mechanism. | In the apo form of csGluDH, K113 (domain I) is hydrogen bound to N373 (domain II) and stabilizes the open structure. On substrate binding, K113 moves to hydrogen bond to the alpha carbonyl of the substrate while maintaining contact with N373. This causes the conformational change which closes the cleft. Based on the crystal structures of csGluDH and previous binding studies with boGluDH, Stillman and Baker, ‘’et al’’ (1993) have proposed the following catalytic mechanism. | ||
After substrate binding and monomer closing, (1) the alpha amino of the glutamate is deprotonated by E165, and (2) hydride transfer to the ‘’Si’’ face of the coenzyme. (3) The change in substrate geometry is sensed by K133and the closed conformation is thought to be brought even closer together to facilitate hydride transfer. (4) Water attacks the iminoketoglutarate intermediate and (5) the protons gained by K125 and D165 in catalysis are lost and the monomer returns to the open conformation. (The Principle of Microreversability dictates that the mechanism for reductive amination can be easily described in a backwards fashion). <ref name="1bgv" /> | After substrate binding and monomer closing, (1) the alpha amino of the glutamate is deprotonated by E165, and (2) hydride transfer to the ‘’Si’’ face of the coenzyme. (3) The change in substrate geometry is sensed by K133and the closed conformation is thought to be brought even closer together to facilitate hydride transfer. (4) Water attacks the iminoketoglutarate intermediate (to become the carbonyl oxygen) and (5) the protons gained by K125 and D165 in catalysis are lost and the monomer returns to the open conformation. (The Principle of Microreversability dictates that the mechanism for reductive amination can be easily described in a backwards fashion). <ref name="1bgv" /> | ||
The details of how ammonia fits into this mechanism remain unknown.<ref name="Lightfoot_1988" /> | |||
==References== | ==References== | ||
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<references /> | <references /> | ||