1TZK

Crystal structure of 1-aminocyclopropane-1-carboxylate-deaminase complexed with alpha-keto-butyrate

Summary for 1TZK

• Entry DOI: 10.2210/pdb1tzk/pdb
• Related: 1RQX 1TYZ 1TZ2 1TZJ 1TZM
• Descriptor: 1-aminocyclopropane-1-carboxylate deaminase, PYRIDOXAL-5'-PHOSPHATE, 2-KETOBUTYRIC ACID, ... (5 entities in total)
• Functional Keywords: accd, complex, crystal, plp, substrate, hydrolase
• Biological source: Pseudomonas sp.
• Total number of polymer chains: 4
• Total formula weight: 148243.81

Authors

Karthikeyan, S.,Zhou, Q.,Zhao, Z.,Kao, C.L.,Tao, Z.,Robinson, H.,Liu, H.W.,Zhang, H. (deposition date: 2004-07-10, release date: 2004-11-02, Last modification date: 2023-11-15)

Primary citation

Karthikeyan, S.,Zhou, Q.,Zhao, Z.,Kao, C.L.,Tao, Z.,Robinson, H.,Liu, H.W.,Zhang, H.
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
Biochemistry, 43:13328-13339, 2004

PubMed Abstract: 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.

PubMed: 15491139
DOI: 10.1021/bi048878g

Experimental method

X-RAY DIFFRACTION (2 Å)