6DGE

Crystal structure of the dimethylarginine dimethylaminohydrolase adduct with N5-(1-imino-2-chloroethyl)-L-lysine

Summary for 6DGE

• Entry DOI: 10.2210/pdb6dge/pdb
• Related: 2JAI 2JAJ 3I2E 3I4A 3P8E 3P8P
• Descriptor: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1, N~6~-[(1E)-2-chloroethanimidoyl]-L-lysine (3 entities in total)
• Functional Keywords: enzyme adduct, hydrolase, covalent inhibitor, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 33845.18

Authors

Monzingo, A.F.,Burstein-Teitelbaum, G.,Er, J.A.V.,Tuley, A.,Fast, W. (deposition date: 2018-05-17, release date: 2018-07-25, Last modification date: 2024-10-23)

Primary citation

Burstein-Teitelbaum, G.,Er, J.A.V.,Monzingo, A.F.,Tuley, A.,Fast, W.
Dissection, Optimization, and Structural Analysis of a Covalent Irreversible DDAH1 Inhibitor.
Biochemistry, 57:4574-4582, 2018

PubMed Abstract: Inhibitors of the human enzyme dimethylarginine dimethylaminohydrolase-1 (DDAH1) can control endogenous nitric oxide production. A time-dependent covalent inactivator of DDAH1, N-(1-imino-2-chloroethyl)-l-ornithine ( K = 1.3 μM, k = 0.34 min), was conceptually dissected into two fragments and each characterized separately: l-norvaline ( K = 470 μM) and 2-chloroacetamidine ( K = 310 μM, k = 4.0 min). This analysis suggested that the two fragments were not linked in a manner that allows either to reach full affinity or reactivity, prompting the synthesis and characterization of three analogues: two that mimic the dimethylation status of the substrate, N-(1-imino-2-chloroisopropyl)-l-ornithine ( k /K = 208 M s) and N-(1-imino-2-chlorisopropyl)-l-lysine ( k /K = 440 M s), and one that lengthens the linker beyond that found in the substrate, N-(1-imino-2-chloroethyl)-l-lysine (Cl-NIL, K = 0.19 μM, k = 0.22 min). Cl-NIL is one of the most potent inhibitors reported for DDAH1, inactivates with a second order rate constant (1.9 × 10 M s) larger than the catalytic efficiency of DDAH1 for its endogenous substrate (1.6 × 10 M s), and has a partition ratio of 1 with a >100 000-fold selectivity for DDAH1 over arginase. An activity-based protein-profiling probe is used to show inhibition of DDAH1 within cultured HEK293T cells (IC = 10 μM) with cytotoxicity appearing only at higher concentrations (ED = 118 μM). A 1.91 Å resolution X-ray crystal structure reveals specific interactions made with DDAH1 upon covalent inactivation by Cl-NIL. Dissecting a covalent inactivator and analysis of its constituent fragments proved useful for the design and optimization of this potent and effective DDAH1 inhibitor.

PubMed: 29983043
DOI: 10.1021/acs.biochem.8b00554

Experimental method

X-RAY DIFFRACTION (1.91 Å)