1PRZ

Crystal structure of pseudouridine synthase RluD catalytic module

Summary for 1PRZ

• Entry DOI: 10.2210/pdb1prz/pdb
• Descriptor: Ribosomal large subunit pseudouridine synthase D (2 entities in total)
• Functional Keywords: pseudouridine synthase, rlud, montreal-kingston bacterial structural genomics initiative, bsgi, structural genomics, lyase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 29229.07

Authors

Sivaraman, J.,Iannuzzi, P.,Cygler, M.,Matte, A.,Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) (deposition date: 2003-06-20, release date: 2003-11-04, Last modification date: 2024-11-06)

Primary citation

Sivaraman, J.,Iannuzzi, P.,Cygler, M.,Matte, A.
Crystal structure of the RluD pseudouridine Synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli
J.Mol.Biol., 335:87-101, 2003

PubMed Abstract: Pseudouridine (5-beta-D-ribofuranosyluracil, Psi) is the most commonly found modified base in RNA. Conversion of uridine to Psi is performed enzymatically in both prokaryotes and eukaryotes by pseudouridine synthases (EC 4.2.1.70). The Escherichia coli Psi-synthase RluD modifies uridine to Psi at positions 1911, 1915 and 1917 within 23S rRNA. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis. Here, we report the crystal structure of the catalytic module of RluD (residues 68-326; DeltaRluD) refined at 1.8A to a final R-factor of 21.8% (R(free)=24.3%). DeltaRluD is a monomeric enzyme having an overall mixed alpha/beta fold. The DeltaRluD molecule consists of two subdomains, a catalytic subdomain and C-terminal subdomain with the RNA-binding cleft formed by loops extending from the catalytic sub-domain. The catalytic sub-domain of DeltaRluD has a similar fold as in TruA, TruB and RsuA, with the location of the RNA-binding cleft, active-site and conserved, catalytic Asp residue superposing in all four structures. Superposition of the crystal structure of TruB bound to a T-stem loop with RluD reveals that similar RNA-protein interactions for the flipped-out uridine base would exist in both structures, implying that base-flipping is necessary for catalysis. This observation also implies that the specificity determinants for site-specific RNA-binding and recognition likely reside in parts of RluD beyond the active site.

PubMed: 14659742
DOI: 10.1016/j.jmb.2003.10.003

Experimental method

X-RAY DIFFRACTION (1.8 Å)