User:Cameron Evans/Sandbox 1
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Unlike the prokaryotic GluDH, mammalian GluDH has been found to always hexamerize as a dimer of | Unlike the prokaryotic GluDH, mammalian GluDH has been found to always hexamerize as a dimer of | ||
<scene name='User:Cameron_Evans/Sandbox_1/Human_d_e_f/1'>trimers</scene>. Also unlike prokaryotic GluDH, the <scene name='User:Cameron_Evans/Sandbox_1/Human_d_alone/1'>monomer</scene> has 48 residue "antenna" that assists in the trimerization process. <scene name='User:Cameron_Evans/Sandbox_1/Human_d_e_f/1'>(The interactions of the antennae are best seen in the trimer)</scene>. These antennae appear to undergo conformational changes as the "mouth" of GluDH opens and closes (see morph below). | <scene name='User:Cameron_Evans/Sandbox_1/Human_d_e_f/1'>trimers</scene>. Also unlike prokaryotic GluDH, the <scene name='User:Cameron_Evans/Sandbox_1/Human_d_alone/1'>monomer</scene> has 48 residue "antenna" that assists in the trimerization process. <scene name='User:Cameron_Evans/Sandbox_1/Human_d_e_f/1'>(The interactions of the antennae are best seen in the trimer)</scene>. These antennae appear to undergo conformational changes as the "mouth" of GluDH opens and closes (see morph below). | ||
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| + | Also unlike prokarytoic GluDH, Mammalian GluDH is allosterically controlled by GTP (-), ATP (-), GDP(+) and ADP(+). Buried proximally (from the center of the protein) to the antennae is the allosteric binding site. | ||
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===Specificity=== | ===Specificity=== | ||
| + | GluDH makes non-coavalent and specific contacts with its substrates, cofactors and allosteric inhibitors. | ||
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| + | For example, glutamate and α-KG both bind via hydrogen bonding within the catalytic cleft between the two distinct clamping domains (see description above in prokaryotes). | ||
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| + | Both make contact with K126, K90, S381, R211, and N349. However, α-KG binding is thought to be stabilized also by N374 and K114 and Glu by K114 in a different crystal structure. | ||
| + | |||
| + | NADH, as it binds within the to the catalytic cleft, makes specific hydrogen bonds with N349, A326 S327 | ||
Revision as of 07:29, 4 April 2010
Glutamate Dehydrogenase
Contents |
General Information
Glutamate Dehydrogenase (GluDH) is a member of the superfamily of amino acid dehydrogenase and functions in the cell to perform they dehydration of α-ketoglutarate to the amino acid glutamate and the reverse reaction.[1]
GluDH feeds α-ketoglutarate into the tricarboxylic acid cycle (TCA) and the amine product is thought to be utilized by other biosynthetic pathways.[2]
Alpha-ketoglutamate.png
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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.
Glutamate dehydrogenase shares sequence homology and structural homology to the superfamily of amino acid dehydrogenases, which suggests divergent evolution. [1]Because of this property among all proteins in the family, many dehydrogenases can work on multiple substrates. GluDH appears to be very specific towards its substrates.[2]
NAD(P)H are cofactors for the reaction and serve to reduce α-KG/ oxidize Glu when they have been reduced. Mammalian GluDH also accomodates allosteric inhibition from GTP and ATP.[2]
Prokaryote
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General Structure
Prokaryotic glutamate dehydrogenase (GDH) does not have any common quaternary structure among crystallized structures (1EUZ is a hexamer, 1HRD a trimer); however, every prokaryotic structure so far elucidated shows a common overall tertiary structure.[1]
Each monomer (reguardless of quaternary structure) has two domains: a domain that is a variant of the Rossmann dinucleotide binding fold (), and a domain involved in oligomerization (when it occurs) and contains most of the substrate binding residues (). [1]
Specificity
is made up of polar interactions from K89 and S380 and hydrophobic interactions from G90, V377 and A163. The last three residues that make this interaction are highly conserved among amino acid dehydrogenases. [1] The polar residues make specific contacts with the glutamine substrate.
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Domain II is in Blue and Domain I is in Purple
Allosteric Interactions
m m m m
...more to come
Eukaryote
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General Structure
Unlike the prokaryotic GluDH, mammalian GluDH has been found to always hexamerize as a dimer of . Also unlike prokaryotic GluDH, the has 48 residue "antenna" that assists in the trimerization process. . These antennae appear to undergo conformational changes as the "mouth" of GluDH opens and closes (see morph below).
Also unlike prokarytoic GluDH, Mammalian GluDH is allosterically controlled by GTP (-), ATP (-), GDP(+) and ADP(+). Buried proximally (from the center of the protein) to the antennae is the allosteric binding site.
Specificity
GluDH makes non-coavalent and specific contacts with its substrates, cofactors and allosteric inhibitors.
For example, glutamate and α-KG both bind via hydrogen bonding within the catalytic cleft between the two distinct clamping domains (see description above in prokaryotes).
Both make contact with K126, K90, S381, R211, and N349. However, α-KG binding is thought to be stabilized also by N374 and K114 and Glu by K114 in a different crystal structure.
NADH, as it binds within the to the catalytic cleft, makes specific hydrogen bonds with N349, A326 S327
Allosteric Interactions
References
- ↑ 1.0 1.1 1.2 1.3 1.4 Stillman TJ, Baker PJ, Britton KL, Rice DW. Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis. J Mol Biol. 1993 Dec 20;234(4):1131-9. PMID:8263917 doi:http://dx.doi.org/10.1006/jmbi.1993.1665
- ↑ 2.0 2.1 2.2 Smith TJ, Peterson PE, Schmidt T, Fang J, Stanley CA. Structures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation. J Mol Biol. 2001 Mar 23;307(2):707-20. PMID:11254391 doi:10.1006/jmbi.2001.4499
