1tzm: Difference between revisions

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Crystal structure of ACC deaminase complexed with substrate analog b-chloro-D-alanine

OverviewOverview

1-Aminocyclopropane-1-carboxylate (ACC) deaminase is a pyridoxal 5'-phosphate (PLP) dependent enzyme catalyzing the opening of the cyclopropane ring of ACC to give alpha-ketobutyric acid and ammonia as the products. This ring cleavage reaction is unusual because the substrate, ACC, contains no abstractable alpha-proton and the carboxyl group is retained in the product. How the reaction is initiated to generate an alpha-carbanionic intermediate, which is the common entry for most PLP-dependent reactions, is not obvious. To gain insight into this unusual ring-opening reaction, we have solved the crystal structures of ACC deaminase from Pseudomonas sp. ACP in complex with substrate ACC, an inhibitor, 1-aminocyclopropane-1-phosphonate (ACP), the product alpha-ketobutyrate, and two d-amino acids. Several notable observations of these structural studies include the following: (1) a typically elusive gem-diamine intermediate is trapped in the enzyme complex with ACC or ACP; (2) Tyr294 is in close proximity (3.0 A) to the pro-S methylene carbon of ACC in the gem-diamine complexes, implicating a direct role of this residue in the ring-opening reaction; (3) Tyr294 may also be responsible for the abstraction of the alpha-proton from d-amino acids, a prelude to the subsequent deamination reaction; (4) the steric hindrance precludes accessibility of active site functional groups to the l-amino acid substrates and may account for the stereospecificity of this enzyme toward d-amino acids. These structural data provide evidence favoring a mechanism in which the ring cleavage is induced by a nucleophilic attack at the pro-S beta-methylene carbon of ACC, with Tyr294 as the nucleophile. However, these observations are also consistent with an alternative mechanistic possibility in which the ring opening is acid-catalyzed and may be facilitated by charge relay through PLP, where Tyr294 functions as a general acid. The results of mutagenesis studies corroborated the assigned critical role for Tyr294 in the catalysis.

About this StructureAbout this Structure

1TZM is a Single protein structure of sequence from Pseudomonas sp. with , , and as ligands. Active as 1-aminocyclopropane-1-carboxylate deaminase, with EC number 3.5.99.7 Full crystallographic information is available from OCA.

ReferenceReference

Structural analysis of Pseudomonas 1-aminocyclopropane-1-carboxylate deaminase complexes: insight into the mechanism of a unique pyridoxal-5'-phosphate dependent cyclopropane ring-opening reaction., Karthikeyan S, Zhou Q, Zhao Z, Kao CL, Tao Z, Robinson H, Liu HW, Zhang H, Biochemistry. 2004 Oct 26;43(42):13328-39. PMID:15491139

Page seeded by OCA on Thu Feb 21 15:19:02 2008

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-[[Image:1tzm.gif|left|200px]]<br /><applet load="1tzm" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1tzm.gif|left|200px]]<br /><applet load="1tzm" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1tzm, resolution 2.08&Aring;" />
 '''Crystal structure of ACC deaminase complexed with substrate analog b-chloro-D-alanine'''<br />
 ==Overview==
--Aminocyclopropane-1-carboxylate (ACC) deaminase is a pyridoxal, 5'-phosphate (PLP) dependent enzyme catalyzing the opening of the, cyclopropane ring of ACC to give alpha-ketobutyric acid and ammonia as the, products. This ring cleavage reaction is unusual because the substrate, ACC, contains no abstractable alpha-proton and the carboxyl group is, retained in the product. How the reaction is initiated to generate an, alpha-carbanionic intermediate, which is the common entry for most, PLP-dependent reactions, is not obvious. To gain insight into this unusual, ring-opening reaction, we have solved the crystal structures of ACC, deaminase from Pseudomonas sp. ACP in complex with substrate ACC, an, inhibitor, 1-aminocyclopropane-1-phosphonate (ACP), the product, alpha-ketobutyrate, and two d-amino acids. Several notable observations of, these structural studies include the following: (1) a typically elusive, gem-diamine intermediate is trapped in the enzyme complex with ACC or ACP;, (2) Tyr294 is in close proximity (3.0 A) to the pro-S methylene carbon of, ACC in the gem-diamine complexes, implicating a direct role of this, residue in the ring-opening reaction; (3) Tyr294 may also be responsible, for the abstraction of the alpha-proton from d-amino acids, a prelude to, the subsequent deamination reaction; (4) the steric hindrance precludes, accessibility of active site functional groups to the l-amino acid, substrates and may account for the stereospecificity of this enzyme toward, d-amino acids. These structural data provide evidence favoring a mechanism, in which the ring cleavage is induced by a nucleophilic attack at the, pro-S beta-methylene carbon of ACC, with Tyr294 as the nucleophile., However, these observations are also consistent with an alternative, mechanistic possibility in which the ring opening is acid-catalyzed and, may be facilitated by charge relay through PLP, where Tyr294 functions as, a general acid. The results of mutagenesis studies corroborated the, assigned critical role for Tyr294 in the catalysis.
+-Aminocyclopropane-1-carboxylate (ACC) deaminase is a pyridoxal 5'-phosphate (PLP) dependent enzyme catalyzing the opening of the cyclopropane ring of ACC to give alpha-ketobutyric acid and ammonia as the products. This ring cleavage reaction is unusual because the substrate, ACC, contains no abstractable alpha-proton and the carboxyl group is retained in the product. How the reaction is initiated to generate an alpha-carbanionic intermediate, which is the common entry for most PLP-dependent reactions, is not obvious. To gain insight into this unusual ring-opening reaction, we have solved the crystal structures of ACC deaminase from Pseudomonas sp. ACP in complex with substrate ACC, an inhibitor, 1-aminocyclopropane-1-phosphonate (ACP), the product alpha-ketobutyrate, and two d-amino acids. Several notable observations of these structural studies include the following: (1) a typically elusive gem-diamine intermediate is trapped in the enzyme complex with ACC or ACP; (2) Tyr294 is in close proximity (3.0 A) to the pro-S methylene carbon of ACC in the gem-diamine complexes, implicating a direct role of this residue in the ring-opening reaction; (3) Tyr294 may also be responsible for the abstraction of the alpha-proton from d-amino acids, a prelude to the subsequent deamination reaction; (4) the steric hindrance precludes accessibility of active site functional groups to the l-amino acid substrates and may account for the stereospecificity of this enzyme toward d-amino acids. These structural data provide evidence favoring a mechanism in which the ring cleavage is induced by a nucleophilic attack at the pro-S beta-methylene carbon of ACC, with Tyr294 as the nucleophile. However, these observations are also consistent with an alternative mechanistic possibility in which the ring opening is acid-catalyzed and may be facilitated by charge relay through PLP, where Tyr294 functions as a general acid. The results of mutagenesis studies corroborated the assigned critical role for Tyr294 in the catalysis.
 ==About this Structure==
-TZM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.] with SO4, PLP, C2N and NAK as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/1-aminocyclopropane-1-carboxylate_deaminase 1-aminocyclopropane-1-carboxylate deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.99.7 3.5.99.7] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1TZM OCA].
+TZM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.] with <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=PLP:'>PLP</scene>, <scene name='pdbligand=C2N:'>C2N</scene> and <scene name='pdbligand=NAK:'>NAK</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/1-aminocyclopropane-1-carboxylate_deaminase 1-aminocyclopropane-1-carboxylate deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.99.7 3.5.99.7] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TZM OCA].
 ==Reference==
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 [[Category: Pseudomonas sp.]]
 [[Category: Single protein]]
-[[Category: Kao, C.L.]]
+[[Category: Kao, C L.]]
 [[Category: Karthikeyan, S.]]
-[[Category: Liu, H.W.]]
+[[Category: Liu, H W.]]
 [[Category: Robinson, H.]]
 [[Category: Tao, Z.]]
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 [[Category: substrate]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 03:43:35 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:19:02 2008''