1maq: Difference between revisions

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CRYSTAL STRUCTURES OF TRUE ENZYMATIC REACTION INTERMEDIATES: ASPARTATE AND GLUTAMATE KETIMINES IN ASPARTATE AMINOTRANSFERASE

OverviewOverview

The crystal structures of the stable, closed complexes of chicken mitochondrial aspartate aminotransferase with the natural substrates L-aspartate and L-glutamate have been solved and refined at 2.4- and 2.3-A resolution, respectively. In both cases, clear electron density at the substrate-coenzyme binding site unequivocally indicates the presence of a covalent intermediate. The crystallographically identical environments of the two subunits of the alpha 2 dimer allow a simple, direct correlation of the coenzyme absorption spectra of the crystalline enzyme with the diffraction results. Deconvolution of the spectra of the crystalline complexes using lognormal curves indicates that the ketimine intermediates constitute 76% and 83% of the total enzyme populations with L-aspartate and L-glutamate, respectively. The electron density maps accommodate the ketimine structures best in agreement with the independent spectral data. Crystalline enzyme has a much higher affinity for keto acid substrates compared to enzyme in solution. The increased affinity is interpreted in terms of a perturbation of the open/closed conformational equilibrium by the crystal lattice, with the closed form having greater affinity for substrate. The crystal lattice contacts provide energy required for domain closure normally supplied by the excess binding energy of the substrate. In solution, enzyme saturated with amino/keto acid substrate pairs has a greater total fraction of intermediates in the aldehyde oxidation state compared to crystalline enzyme. Assuming the only difference between the solution and crystalline enzymes is in conformational freedom, this difference suggests that one or more substantially populated, aldehydic intermediates in solution exist in the open conformation. Quantitative analyses of the spectra indicate that the value of the equilibrium constant for the open-closed conformational transition of the liganded, aldehydic enzyme in solution is near 1. The C4' pro-S proton in the ketimine models is oriented nearly perpendicularly to the plane of the pyridine ring, suggesting that the enzyme facilitates its removal by maximizing sigma-pi orbital overlap. The absence of a localized water molecule near Lys258 dictates that ketimine hydrolysis occurs via a transiently bound water molecule or from an alternative, possibly more open, structure in which water is appropriately bound. A prominent mechanistic role for flexibility of the Lys258 side chain is suggested by the absence of hydrogen bonds to the amino group in the aspartate structure and the relatively high temperature factors for these atoms in both structures.

About this StructureAbout this Structure

1MAQ is a Single protein structure of sequence from Gallus gallus with as ligand. Active as Aspartate transaminase, with EC number 2.6.1.1 Full crystallographic information is available from OCA.

ReferenceReference

Crystal structures of true enzymatic reaction intermediates: aspartate and glutamate ketimines in aspartate aminotransferase., Malashkevich VN, Toney MD, Jansonius JN, Biochemistry. 1993 Dec 14;32(49):13451-62. PMID:7903048

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-[[Image:1maq.jpg|left|200px]]<br /><applet load="1maq" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1maq.jpg|left|200px]]<br /><applet load="1maq" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1maq, resolution 2.3&Aring;" />
 '''CRYSTAL STRUCTURES OF TRUE ENZYMATIC REACTION INTERMEDIATES: ASPARTATE AND GLUTAMATE KETIMINES IN ASPARTATE AMINOTRANSFERASE'''<br />
 ==Overview==
-The crystal structures of the stable, closed complexes of chicken, mitochondrial aspartate aminotransferase with the natural substrates, L-aspartate and L-glutamate have been solved and refined at 2.4- and 2.3-A, resolution, respectively. In both cases, clear electron density at the, substrate-coenzyme binding site unequivocally indicates the presence of a, covalent intermediate. The crystallographically identical environments of, the two subunits of the alpha 2 dimer allow a simple, direct correlation, of the coenzyme absorption spectra of the crystalline enzyme with the, diffraction results. Deconvolution of the spectra of the crystalline, complexes using lognormal curves indicates that the ketimine intermediates, constitute 76% and 83% of the total enzyme populations with L-aspartate, and L-glutamate, respectively. The electron density maps accommodate the, ketimine structures best in agreement with the independent spectral data., Crystalline enzyme has a much higher affinity for keto acid substrates, compared to enzyme in solution. The increased affinity is interpreted in, terms of a perturbation of the open/closed conformational equilibrium by, the crystal lattice, with the closed form having greater affinity for, substrate. The crystal lattice contacts provide energy required for domain, closure normally supplied by the excess binding energy of the substrate., In solution, enzyme saturated with amino/keto acid substrate pairs has a, greater total fraction of intermediates in the aldehyde oxidation state, compared to crystalline enzyme. Assuming the only difference between the, solution and crystalline enzymes is in conformational freedom, this, difference suggests that one or more substantially populated, aldehydic, intermediates in solution exist in the open conformation. Quantitative, analyses of the spectra indicate that the value of the equilibrium, constant for the open-closed conformational transition of the liganded, aldehydic enzyme in solution is near 1. The C4' pro-S proton in the, ketimine models is oriented nearly perpendicularly to the plane of the, pyridine ring, suggesting that the enzyme facilitates its removal by, maximizing sigma-pi orbital overlap. The absence of a localized water, molecule near Lys258 dictates that ketimine hydrolysis occurs via a, transiently bound water molecule or from an alternative, possibly more, open, structure in which water is appropriately bound. A prominent, mechanistic role for flexibility of the Lys258 side chain is suggested by, the absence of hydrogen bonds to the amino group in the aspartate, structure and the relatively high temperature factors for these atoms in, both structures.
+The crystal structures of the stable, closed complexes of chicken mitochondrial aspartate aminotransferase with the natural substrates L-aspartate and L-glutamate have been solved and refined at 2.4- and 2.3-A resolution, respectively. In both cases, clear electron density at the substrate-coenzyme binding site unequivocally indicates the presence of a covalent intermediate. The crystallographically identical environments of the two subunits of the alpha 2 dimer allow a simple, direct correlation of the coenzyme absorption spectra of the crystalline enzyme with the diffraction results. Deconvolution of the spectra of the crystalline complexes using lognormal curves indicates that the ketimine intermediates constitute 76% and 83% of the total enzyme populations with L-aspartate and L-glutamate, respectively. The electron density maps accommodate the ketimine structures best in agreement with the independent spectral data. Crystalline enzyme has a much higher affinity for keto acid substrates compared to enzyme in solution. The increased affinity is interpreted in terms of a perturbation of the open/closed conformational equilibrium by the crystal lattice, with the closed form having greater affinity for substrate. The crystal lattice contacts provide energy required for domain closure normally supplied by the excess binding energy of the substrate. In solution, enzyme saturated with amino/keto acid substrate pairs has a greater total fraction of intermediates in the aldehyde oxidation state compared to crystalline enzyme. Assuming the only difference between the solution and crystalline enzymes is in conformational freedom, this difference suggests that one or more substantially populated, aldehydic intermediates in solution exist in the open conformation. Quantitative analyses of the spectra indicate that the value of the equilibrium constant for the open-closed conformational transition of the liganded, aldehydic enzyme in solution is near 1. The C4' pro-S proton in the ketimine models is oriented nearly perpendicularly to the plane of the pyridine ring, suggesting that the enzyme facilitates its removal by maximizing sigma-pi orbital overlap. The absence of a localized water molecule near Lys258 dictates that ketimine hydrolysis occurs via a transiently bound water molecule or from an alternative, possibly more open, structure in which water is appropriately bound. A prominent mechanistic role for flexibility of the Lys258 side chain is suggested by the absence of hydrogen bonds to the amino group in the aspartate structure and the relatively high temperature factors for these atoms in both structures.
 ==About this Structure==
-MAQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] with PGU as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Aspartate_transaminase Aspartate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.1 2.6.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1MAQ OCA].
+MAQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] with <scene name='pdbligand=PGU:'>PGU</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Aspartate_transaminase Aspartate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.1 2.6.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MAQ OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Gallus gallus]]
 [[Category: Single protein]]
-[[Category: Jansonius, J.N.]]
+[[Category: Jansonius, J N.]]
-[[Category: Malashkevich, V.N.]]
+[[Category: Malashkevich, V N.]]
 [[Category: PGU]]
 [[Category: aminotransferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:16:56 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:53:26 2008''