4OHB

Crystal structure of MilB E103A in complex with 5-hydroxymethylcytidine 5'-monophosphate (hmCMP) from Streptomyces rimofaciens

4OHB の概要

• エントリーDOI: 10.2210/pdb4ohb/pdb
• 関連するPDBエントリー: 4OHR
• 分子名称: CMP/hydroxymethyl CMP hydrolase, 5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate) (3 entities in total)
• 機能のキーワード: hydrolase, protein-hmcmp complex
• 由来する生物種: Streptomyces rimofaciens
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 20823.21

構造登録者

Zhao, G.,Zhang, Y.,Liu, G.,Wu, G.,He, X. (登録日: 2014-01-17, 公開日: 2014-06-25, 最終更新日: 2024-03-20)

主引用文献

Zhao, G.,Wu, G.,Zhang, Y.,Liu, G.,Han, T.,Deng, Z.,He, X.
Structure of the N-glycosidase MilB in complex with hydroxymethyl CMP reveals its Arg23 specifically recognizes the substrate and controls its entry
Nucleic Acids Res., 42:8115-8124, 2014

PubMed Abstract: 5-Hydroxymethylcytosine (5hmC) is present in T-even phage and mammalian DNA as well as some nucleoside antibiotics, including mildiomycin and bacimethrin, during whose synthesis 5hmC is produced by the hydrolysis of 5-hydroxymethyl cytidine 5'-monophosphate (hmCMP) by an N-glycosidase MilB. Recently, the MilB-CMP complex structure revealed its substrate specificity for CMP over dCMP. However, hmCMP instead of CMP is the preferred substrate for MilB as supported by that its KM for CMP is ∼27-fold higher than that for hmCMP. Here, we determined the crystal structures of MilB and its catalytically inactive E103A mutant in complex with hmCMP. In the structure of the complex, Phe22 and Arg23 are positioned in a cage-like active site resembling the binding pocket for the flipped 5-methylcytosine (5mC) in eukaryotic 5mC-binding proteins. Van der Waals interaction between the benzene ring of Phe22 and the pyrimidine ring of hmCMP stabilizes its binding. Remarkably, upon hmCMP binding, the guanidinium group of Arg23 was bent ∼65° toward hmCMP to recognize its 5-hydroxymethyl group, inducing semi-closure of the cage-like pocket. Mutagenesis studies of Arg23 and bioinformatics analysis demonstrate that the positively charged Arg/Lys at this site is critical for the specific recognition of the 5-hydroxymethyl group of hmCMP.

PubMed: 24920828
DOI: 10.1093/nar/gku486

実験手法

X-RAY DIFFRACTION (2.4 Å)