Sandbox Reserved 660: Difference between revisions

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The AMP <scene name='Sandbox_Reserved_660/Act_site/1'>binding pocket</scene> is mainly located within the N-domain. The highly conserved sequence which corresponds to <scene name='Sandbox_Reserved_660/Binding_site/1'>Q328GYGMTEA335</scene> in 4CL provides the majority of the surface of the binding pocket. The side chain phenyl group of Tyr-330 provide the Van Der Waals interaction to the adenine group of the bound AMP on one side of the adenine ring and on the other side, the adenine group is support by the side chain of Gly-306 and main chain of Ala-307. The N atoms of adenine group could also donate hydrogen bond to the carbonyl oxygen of Gly-329. Several hydrogen bonds are formed between the ribose oxygen atoms and the side chains of Arg-432, Lys-434, and Lys-438 and the phosphate group could also form hydrogen bond with side chain of Thr-333 and Gln-443 and main chain NH of Thr-333[3].

The <scene name='Sandbox_Reserved_660/Cata_site/1'>Catalytic site</scene> of the 4CL is located on Lys-523 on the C domain and Lys-438 and Gln-443 on the N domain. there is a Ligand Binding–Induced Conformational Changes~~, and the conformational changes, was~~ observed in 4CL1 structures upon the binding of AMP. A large cleft was observed between the N- and C-domains in apo-4CL1 (unmodified) and the cleft is closed by an 81˚ rotation of the C-domain relative to the N-domain ~~upon~~ the AMP binding. Because no major internal changes are found in either the N- or C-domain, the closure of the inter domain cleft upon the binding of AMP is a rigid-body movement[4]. The Inter domain movement brings different catalytic residues from the C-domains to substrate binding sites to catalyze the respective partial reactions, such as the adenylate-forming partial reaction, and the thioester-forming partial reaction.

The <scene name='Sandbox_Reserved_660/Cata_site/1'>Catalytic site</scene> of the 4CL is located on Lys-523 within the C domain and Lys-438 and Gln-443 within the N domain. there is a Ligand Binding–Induced Conformational Changes observed in 4CL1 structures upon the binding of AMP. A large cleft was observed between the N- and C-domains in apo-4CL1 (unmodified) and the cleft is closed by an 81˚ rotation of the C-domain relative to the N-domain when the ligand AMP is bound to the binding pocket. Because no major internal conformation or structure changes are found in either the N- or C-domain, the closure of the inter domain cleft upon the binding of AMP is a rigid-body movement[4]. The Inter domain movement brings different catalytic residues (i.e. Lys-523) from the C-domains to substrate binding sites to catalyze the respective partial reactions, such as the adenylate-forming partial reaction, and the thioester-forming partial reaction.

==Enzymatic Mechanism==

The ~~mechanism~~ begins with the binding of ATP and hydroxycinnamate substrates. The binding results in 4CL1 adopting the catalytic conformation for the adenylate-forming partial reaction, in which the side chain of Lys-523 interacts with and directs the carboxylate group of the bound hydroxycinnamates for the nucleophilic attack of the α-phosphate of ATP, resulting in an AMP-hydroxycinnamate conjugate and a PPi molecule. The release of PPi then propels 4CL1 to the catalytic conformation of the thioester-forming partial reaction. In this conformation, the side chain of His-234 swings aside to allow access of CoA to the AMP-hydroxycinnamate conjugate. The AMP-hydroxycinnamate conjugate and CoA are then catalyzed by side chains of Lys-438 and Gln-443 to form the ﬁnal thioester product. The C-domain rotates again to expose the substrate binding site, and the thioester and AMP are released[3].

The enzymaticmechanism begins with the binding of ATP and hydroxycinnamate substrates. The binding results in 4CL1 adopting the catalytic conformation for the adenylate-forming partial reaction, in which the side chain of Lys-523 interacts with and directs the carboxylate group of the bound hydroxycinnamates for the nucleophilic attack of the α-phosphate of ATP, resulting in an AMP-hydroxycinnamate conjugate and a PPi molecule. The release of PPi then propels 4CL1 to the catalytic conformation of the thioester-forming partial reaction. In this conformation, the side chain of His-234 swings aside to allow access of CoA to the AMP-hydroxycinnamate conjugate. The AMP-hydroxycinnamate conjugate and CoA are then catalyzed by side chains of Lys-438 and Gln-443 to form the ﬁnal thioester product. The C-domain rotates again to expose the substrate binding site, and the thioester and AMP are released[3].

==Implication==

4-Coumarate-coenzyme A ligase (4CL) is an enzyme that functions early in the general phenylpropanoid pathway by producing the monolignol precursor p-coumaroyl-CoA. 4CL silencing in angiosperm species such as tobacco, Arabidopsis and Populus tremuloides causes lignin reductions in the range of 25% to 45%. However, the impacts of these manipulations on lignin composition varied. 4CL silencing in tobacco preferentially depleted ~~syringyl~~ (S) lignin units, which are prominent in wood fibers. 4CL silencing in Arabidopsis depleted only ~~guaiacyl~~ (G) lignin units, which are enriched in vessel elements, whereas silencing of 4CL in P.tremuloides had no impact on the S-G ratio. An increase in the S-G ratio in P.tremuloides was only recorded when 4CL silencing was combined with the over expression of coniferaldehyde 5-hydroxylase. These differences in lignin composition could be the consequence of silencing 4CL isoforms with different substrate preferences, or they could reflect the in adequacies or limitations of analytical procedures used for lignin analysis[5].

4-Coumarate-coenzyme A ligase (4CL) is an enzyme that functions early in the general phenylpropanoid pathway by producing the monolignol precursor p-coumaroyl-CoA. 4CL silencing in angiosperm species such as tobacco, Arabidopsis and Populus tremuloides causes lignin reductions in the range of 25% to 45%. However, the impacts of these manipulations on lignin composition varied. 4CL silencing in tobacco preferentially depleted sinapyl (S) lignin units, which are prominent in wood fibers. 4CL silencing in Arabidopsis depleted only coniferyl (G) lignin units, which are enriched in vessel elements, whereas silencing of 4CL in P.tremuloides had no impact on the S-G ratio. An increase in the S-G ratio in P.tremuloides was only recorded when 4CL silencing was combined with the over expression of coniferaldehyde 5-hydroxylase. These differences in lignin composition could be the consequence of silencing 4CL isoforms with different substrate preferences, or they could reflect the in adequacies or limitations of analytical procedures used for lignin analysis[5].

Sandbox Reserved 660: Difference between revisions

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 The AMP <scene name='Sandbox_Reserved_660/Act_site/1'>binding pocket</scene> is mainly located within the N-domain. The highly conserved sequence which corresponds to <scene name='Sandbox_Reserved_660/Binding_site/1'>Q328GYGMTEA335</scene> in 4CL provides the majority of the surface of the binding pocket. The side chain phenyl group of Tyr-330 provide the Van Der Waals interaction to the adenine group of the bound AMP on one side of the adenine ring and on the other side, the adenine group is support by the side chain of Gly-306 and main chain of Ala-307. The N atoms of adenine group could also donate hydrogen bond to the carbonyl oxygen of Gly-329. Several hydrogen bonds are formed between the ribose oxygen atoms and the side chains of Arg-432, Lys-434, and Lys-438 and the phosphate group could also form hydrogen bond with side chain of Thr-333 and Gln-443 and main chain NH of Thr-333[3].
-The <scene name='Sandbox_Reserved_660/Cata_site/1'>Catalytic site</scene> of the 4CL is located on Lys-523 on the C domain and Lys-438 and Gln-443 on the N domain. there  is a Ligand Binding–Induced Conformational Changes,  and the conformational changes, was observed in 4CL1 structures upon the binding of AMP. A large cleft was observed between the N- and C-domains in apo-4CL1 (unmodified) and the cleft is closed by an 81˚ rotation of the C-domain relative to the N-domain upon the AMP binding. Because no major internal changes are found in either the N- or C-domain, the closure of the inter domain cleft upon the binding of AMP is a rigid-body movement[4]. The Inter domain movement brings different catalytic residues from the C-domains to substrate binding sites to catalyze the respective partial reactions, such as the adenylate-forming partial reaction, and the thioester-forming partial reaction.
+The <scene name='Sandbox_Reserved_660/Cata_site/1'>Catalytic site</scene> of the 4CL is located on Lys-523 within the C domain and Lys-438 and Gln-443 within the N domain. there  is a Ligand Binding–Induced Conformational Changes observed in 4CL1 structures upon the binding of AMP. A large cleft was observed between the N- and C-domains in apo-4CL1 (unmodified) and the cleft is closed by an 81˚ rotation of the C-domain relative to the N-domain when the ligand AMP is bound to the binding pocket. Because no major internal conformation or structure changes are found in either the N- or C-domain, the closure of the inter domain cleft upon the binding of AMP is a rigid-body movement[4]. The Inter domain movement brings different catalytic residues (i.e. Lys-523) from the C-domains to substrate binding sites to catalyze the respective partial reactions, such as the adenylate-forming partial reaction, and the thioester-forming partial reaction.
 ==Enzymatic Mechanism==
-The mechanism begins with the binding of ATP and hydroxycinnamate substrates. The binding results in 4CL1 adopting the catalytic conformation for the adenylate-forming partial reaction, in which the side chain of Lys-523 interacts with and directs the carboxylate group of the bound  hydroxycinnamates  for  the  nucleophilic  attack  of  the α-phosphate  of  ATP,  resulting  in  an  AMP-hydroxycinnamate conjugate and a PPi molecule. The release of PPi then propels 4CL1  to  the  catalytic  conformation  of  the  thioester-forming partial reaction.  In this conformation,  the side chain of His-234 swings aside to allow access of CoA to the AMP-hydroxycinnamate conjugate. The AMP-hydroxycinnamate conjugate and CoA are then catalyzed by side chains of Lys-438 and Gln-443 to form the ﬁnal thioester product. The C-domain rotates again to expose the substrate binding site, and the thioester and AMP are released[3].
+The enzymaticmechanism begins with the binding of ATP and hydroxycinnamate substrates. The binding results in 4CL1 adopting the catalytic conformation for the adenylate-forming partial reaction, in which the side chain of Lys-523 interacts with and directs the carboxylate group of the bound  hydroxycinnamates  for  the  nucleophilic  attack  of  the α-phosphate  of  ATP,  resulting  in  an  AMP-hydroxycinnamate conjugate and a PPi molecule. The release of PPi then propels 4CL1  to  the  catalytic  conformation  of  the  thioester-forming partial reaction.  In this conformation,  the side chain of His-234 swings aside to allow access of CoA to the AMP-hydroxycinnamate conjugate. The AMP-hydroxycinnamate conjugate and CoA are then catalyzed by side chains of Lys-438 and Gln-443 to form the ﬁnal thioester product. The C-domain rotates again to expose the substrate binding site, and the thioester and AMP are released[3].
 ==Implication==
--Coumarate-coenzyme A ligase (4CL) is an enzyme that functions early in the general  phenylpropanoid pathway by producing the monolignol precursor p-coumaroyl-CoA. 4CL silencing in angiosperm species such as tobacco, Arabidopsis and Populus tremuloides causes lignin reductions in the range of 25% to 45%. However, the impacts of these manipulations on lignin composition varied. 4CL silencing in tobacco preferentially depleted syringyl (S) lignin units, which are prominent in wood fibers. 4CL silencing in Arabidopsis depleted only guaiacyl (G) lignin units, which are enriched in vessel elements, whereas silencing of 4CL in P.tremuloides had no impact on the S-G ratio. An increase in the S-G ratio in P.tremuloides was only recorded when 4CL silencing was combined with the over expression of coniferaldehyde 5-hydroxylase. These differences in lignin composition could be the consequence of silencing 4CL isoforms with different substrate preferences, or they could reflect the in adequacies or limitations of analytical procedures used for lignin analysis[5].
+-Coumarate-coenzyme A ligase (4CL) is an enzyme that functions early in the general  phenylpropanoid pathway by producing the monolignol precursor p-coumaroyl-CoA. 4CL silencing in angiosperm species such as tobacco, Arabidopsis and Populus tremuloides causes lignin reductions in the range of 25% to 45%. However, the impacts of these manipulations on lignin composition varied. 4CL silencing in tobacco preferentially depleted sinapyl (S) lignin units, which are prominent in wood fibers. 4CL silencing in Arabidopsis depleted only coniferyl (G) lignin units, which are enriched in vessel elements, whereas silencing of 4CL in P.tremuloides had no impact on the S-G ratio. An increase in the S-G ratio in P.tremuloides was only recorded when 4CL silencing was combined with the over expression of coniferaldehyde 5-hydroxylase. These differences in lignin composition could be the consequence of silencing 4CL isoforms with different substrate preferences, or they could reflect the in adequacies or limitations of analytical procedures used for lignin analysis[5].