3lwp is a 5 chain structure with sequence from Atcc 43587. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
[TRUB_PYRFU] Could be responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs (By similarity). [RL7A_PYRFU] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs (By similarity). [NOP10_PYRFU] Involved in ribosome biogenesis; more specifically in 18S rRNA pseudouridylation and in cleavage of pre-rRNA (By similarity).
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The most abundant chemical modification on RNA is isomerization of uridine (or pseudouridylation) catalyzed by pseudouridine synthases. The catalytic mechanism of this essential process remains largely speculative, partly due to lack of knowledge of the pre-reactive state that is important to the identification of reactive chemical moieties. In the present study, we showed, using orthogonal space random-walk free-energy simulation, that the pre-reactive states of uridine and its reactive derivative 5-fluorouridine, bound to a ribonucleoprotein particle pseudouridine synthase, strongly prefer the syn glycosidic bond conformation, while that of the nonreactive 5-bromouridine-containing substrate is largely populated in the anti conformation state. A high-resolution crystal structure of the 5-bromouridine-containing substrate bound to the ribonucleoprotein particle pseudouridine synthase and enzyme activity assay confirmed the anti nonreactive conformation and provided the molecular basis for its confinement. The observed preference for the syn pre-reactive state by the enzyme-bound uridine may help to distinguish among currently proposed mechanisms.
Glycosidic bond conformation preference plays a pivotal role in catalysis of RNA pseudouridylation: a combined simulation and structural study.,Zhou J, Lv C, Liang B, Chen M, Yang W, Li H J Mol Biol. 2010 Sep 3;401(5):690-5. Epub 2010 Jul 6. PMID:20615421[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
↑Zhou J, Lv C, Liang B, Chen M, Yang W, Li H. Glycosidic bond conformation preference plays a pivotal role in catalysis of RNA pseudouridylation: a combined simulation and structural study. J Mol Biol. 2010 Sep 3;401(5):690-5. Epub 2010 Jul 6. PMID:20615421 doi:10.1016/j.jmb.2010.06.061
