TY - JOUR
T1 - Solution Structure of RCL, a Novel 2′-Deoxyribonucleoside 5′-Monophosphate N-glycosidase
AU - Doddapaneni, Kiran
AU - Mahler, Bryon
AU - Pavlovicz, Ryan
AU - Haushalter, Adam
AU - Yuan, Chunhua
AU - Wu, Zhengrong
N1 - Funding Information:
We thank Prof. Steven E. Ealick and Dr. P. Alexandre Kaminski for the RCL plasmid, and Dr. Chenglong Li for useful discussions. We are also grateful for the CPU time provided by Ohio Supercomputer Center. R. Pavlovicz was supported by AFPE fellowship, and this work was funded in part by NIH R21EY018423 and NSF MCB-0719264.
PY - 2009/12/4
Y1 - 2009/12/4
N2 - RCL is an enzyme that catalyzes the N-glycosidic bond cleavage of purine 2′-deoxyribonucleoside 5′-monophosphates, a novel enzymatic reaction reported only recently. In this work, we determined the solution structure by multidimensional NMR and provide a structural framework to elucidate its mechanism with computational simulation. RCL is a symmetric homodimer, with each monomer consisting of a five-stranded parallel β-sheet sandwiched between five α-helices. Three of the helices form the dimer interface, allowing two monomers to pack side by side. The overall architecture featuring a Rossmann fold is topologically similar to that of deoxyribosyltransferases, with major differences observed in the putative substrate binding pocket and the C-terminal tail. The latter is seemingly flexible and projecting away from the core structure in RCL, but loops back and is positioned at the bottom of the neighboring active site in the transferases. This difference may bear functional implications in the context of nucleobase recognition involving the C-terminal carboxyl group, which is only required in the reverse reaction by the transferases. It was also noticed that residues around the putative active site show significant conformational variation, suggesting that protein dynamics may play an important role in the enzymatic function of apo-RCL. Overall, the work provides invaluable insight into the mechanism of a novel N-glycosidase from the structural point of view, which in turn will allow rational anti-tumor and anti-angiogenesis drug design.
AB - RCL is an enzyme that catalyzes the N-glycosidic bond cleavage of purine 2′-deoxyribonucleoside 5′-monophosphates, a novel enzymatic reaction reported only recently. In this work, we determined the solution structure by multidimensional NMR and provide a structural framework to elucidate its mechanism with computational simulation. RCL is a symmetric homodimer, with each monomer consisting of a five-stranded parallel β-sheet sandwiched between five α-helices. Three of the helices form the dimer interface, allowing two monomers to pack side by side. The overall architecture featuring a Rossmann fold is topologically similar to that of deoxyribosyltransferases, with major differences observed in the putative substrate binding pocket and the C-terminal tail. The latter is seemingly flexible and projecting away from the core structure in RCL, but loops back and is positioned at the bottom of the neighboring active site in the transferases. This difference may bear functional implications in the context of nucleobase recognition involving the C-terminal carboxyl group, which is only required in the reverse reaction by the transferases. It was also noticed that residues around the putative active site show significant conformational variation, suggesting that protein dynamics may play an important role in the enzymatic function of apo-RCL. Overall, the work provides invaluable insight into the mechanism of a novel N-glycosidase from the structural point of view, which in turn will allow rational anti-tumor and anti-angiogenesis drug design.
KW - N-glycosidase
KW - RCL
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U2 - 10.1016/j.jmb.2009.08.054
DO - 10.1016/j.jmb.2009.08.054
M3 - Article
C2 - 19720067
AN - SCOPUS:70449534068
SN - 0022-2836
VL - 394
SP - 423
EP - 434
JO - Journal of Molecular Biology
JF - Journal of Molecular Biology
IS - 3
ER -