1QYU
Structure of the catalytic domain of 23S rRNA pseudouridine synthase RluD
Summary for 1QYU
| Entry DOI | 10.2210/pdb1qyu/pdb |
| Descriptor | Ribosomal large subunit pseudouridine synthase D (2 entities in total) |
| Functional Keywords | catalytic domain, rlud, pseudouridine synthase, lyase |
| Biological source | Escherichia coli |
| Total number of polymer chains | 1 |
| Total formula weight | 40250.99 |
| Authors | Del Campo, M.,Ofengand, J.,Malhotra, A. (deposition date: 2003-09-12, release date: 2003-12-09, Last modification date: 2024-11-20) |
| Primary citation | Del Campo, M.,Ofengand, J.,Malhotra, A. Crystal structure of the catalytic domain of RluD, the only rRNA pseudouridine synthase required for normal growth of Escherichia coli RNA, 10:231-239, 2004 Cited by PubMed Abstract: Escherichia coli pseudouridine synthase RluD makes pseudouridines 1911, 1915, and 1917 in the loop of helix 69 in 23S RNA. These are the most highly conserved ribosomal pseudouridines known. Of 11 pseudouridine synthases in E. coli, only cells lacking RluD have severe growth defects and abnormal ribosomes. We have determined the 2.0 A structure of the catalytic domain of RluD (residues 77-326), the first structure of an RluA family member. The catalytic domain folds into a mainly antiparallel beta-sheet flanked by several loops and helices. A positively charged cleft that presumably binds RNA leads to the conserved Asp 139. The RluD N-terminal S4 domain, connected by a flexible linker, is disordered in our structure. RluD is very similar in both catalytic domain structure and active site arrangement to the pseudouridine synthases RsuA, TruB, and TruA. We identify five sequence motifs, two of which are novel, in the RluA, RsuA, TruB, and TruA families, uniting them as one superfamily. These results strongly suggest that four of the five families of pseudouridine synthases arose by divergent evolution. The RluD structure also provides insight into its multisite specificity. PubMed: 14730022DOI: 10.1261/rna.5187404 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2 Å) |
Structure validation
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