5K9N

Structural and Mechanistic Analysis of Drosophila melanogaster Polyamine N acetyltransferase, an enzyme that Catalyzes the Formation of N acetylagmatine

Summary for 5K9N

• Entry DOI: 10.2210/pdb5k9n/pdb
• Descriptor: Polyamine N acetyltransferase (2 entities in total)
• Functional Keywords: polyamine n acetyltransferase, agmatine, n acetylagmatine, drosophila melanogaster, enzyme mechanism, acetyl-coa, and protein crystallography, transferase
• Biological source: Drosophila melanogaster (Fruit fly)
• Total number of polymer chains: 2
• Total formula weight: 47598.22

Authors

Dempsey, D.R.,Nichols, D.A.,Battistini, M.R.,Pemberton, O.,Ospina, S.R.,Zhang, X.,Carpenter, A.-M.,Chen, Y.,Merkler, D.J. (deposition date: 2016-06-01, release date: 2017-06-07, Last modification date: 2024-02-28)

Primary citation

Dempsey, D.R.,Nichols, D.A.,Battistini, M.R.,Pemberton, O.,Ospina, S.R.,Zhang, X.,Carpenter, A.M.,O'Flynn, B.G.,Leahy, J.W.,Kanwar, A.,Lewandowski, E.M.,Chen, Y.,Merkler, D.J.
Structural and Mechanistic Analysis of Drosophila melanogaster Agmatine N-Acetyltransferase, an Enzyme that Catalyzes the Formation of N-Acetylagmatine.
Sci Rep, 7:13432-13432, 2017

PubMed Abstract: Agmatine N-acetyltransferase (AgmNAT) catalyzes the formation of N-acetylagmatine from acetyl-CoA and agmatine. Herein, we provide evidence that Drosophila melanogaster AgmNAT (CG15766) catalyzes the formation of N-acetylagmatine using an ordered sequential mechanism; acetyl-CoA binds prior to agmatine to generate an AgmNAT•acetyl-CoA•agmatine ternary complex prior to catalysis. Additionally, we solved a crystal structure for the apo form of AgmNAT with an atomic resolution of 2.3 Å, which points towards specific amino acids that may function in catalysis or active site formation. Using the crystal structure, primary sequence alignment, pH-activity profiles, and site-directed mutagenesis, we evaluated a series of active site amino acids in order to assign their functional roles in AgmNAT. More specifically, pH-activity profiles identified at least one catalytically important, ionizable group with an apparent pK of ~7.5, which corresponds to the general base in catalysis, Glu-34. Moreover, these data led to a proposed chemical mechanism, which is consistent with the structure and our biochemical analysis of AgmNAT.

PubMed: 29044148
DOI: 10.1038/s41598-017-13669-6

Experimental method

X-RAY DIFFRACTION (2.3 Å)