4HFQ

Crystal structure of UDP-X diphosphatase

4HFQ の概要

• エントリーDOI: 10.2210/pdb4hfq/pdb
• 分子名称: MutT/nudix family protein, 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (8 entities in total)
• 機能のキーワード: udp-sugar diphosphatase, nudix, hydrolase, rna exonuclease, pyrophosphatase, mur pathway
• 由来する生物種: Streptococcus pneumoniae
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 49643.62

構造登録者

Duong-Ly, K.C.,Amzel, L.M.,Gabelli, S.B. (登録日: 2012-10-05, 公開日: 2013-08-07, 最終更新日: 2024-02-28)

主引用文献

Duong-Ly, K.C.,Woo, H.N.,Dunn, C.A.,Xu, W.,Babic, A.,Bessman, M.J.,Amzel, L.M.,Gabelli, S.B.
A UDP-X diphosphatase from Streptococcus pneumoniae hydrolyzes precursors of peptidoglycan biosynthesis.
Plos One, 8:e64241-e64241, 2013

PubMed Abstract: The gene for a Nudix enzyme (SP_1669) was found to code for a UDP-X diphosphatase. The SP_1669 gene is localized among genes encoding proteins that participate in cell division in Streptococcus pneumoniae. One of these genes, MurF, encodes an enzyme that catalyzes the last step of the Mur pathway of peptidoglycan biosynthesis. Mur pathway substrates are all derived from UDP-glucosamine and all are potential Nudix substrates. We showed that UDP-X diphosphatase can hydrolyze the Mur pathway substrates UDP-N-acetylmuramic acid and UDP-N-acetylmuramoyl-L-alanine. The 1.39 Å resolution crystal structure of this enzyme shows that it folds as an asymmetric homodimer with two distinct active sites, each containing elements of the conserved Nudix box sequence. In addition to its Nudix catalytic activity, the enzyme has a 3'5' RNA exonuclease activity. We propose that the structural asymmetry in UDP-X diphosphatase facilitates the recognition of these two distinct classes of substrates, Nudix substrates and RNA. UDP-X diphosphatase is a prototype of a new family of Nudix enzymes with unique structural characteristics: two monomers, each consisting of an N-terminal helix bundle domain and a C-terminal Nudix domain, form an asymmetric dimer with two distinct active sites. These enzymes function to hydrolyze bacterial cell wall precursors and degrade RNA.

PubMed: 23691178
DOI: 10.1371/journal.pone.0064241

実験手法

X-RAY DIFFRACTION (1.39 Å)