⊟Summary[edit | edit source]
- pan ID?: SAUPAN003477000
- symbol?: —
- synonym:
- description?: RluA family pseudouridine synthase
- RluA family pseudouridine synthase
- pseudouridine synthase, RluA family
- pseudouridylate synthase
- ribosomal large subunit pseudouridine synthase D
- Pseudouridine synthase
- pseudouridylate synthase RluD
- putative RNA pseudouridylate synthase
- ribosomal large subunit psudouridine synthase D
- RluD subfamily ribosomal large subunit pseudouridine synthase
descriptions from strain specific annotations:
- strand?: +
- coordinates?: 3816163..3817080
- synteny block?: BlockID0025560
- occurrence?: in 100% of 34 strains
rluD : ribosomal large subunit pseudouridine synthase D [1]
Although very few post-transcriptional ribosomal RNA modifications are absolutely required for functional protein synthesis, many residues can be modified to enhance the stability, fidelity and rate of reaction. One such modification is the isomerization of uridines in 23S rRNA at positions 1911, 1915 and 1917 (E. coli numbering; 1938, 1942 and 1944 by S. aureus numbering) into pseudouridines by pseudouridine synthase/isomerase D.
RluD is a member of the RluA-like family of pseudouridine synthases (ΨS). There are four potential RluA-like ΨS enzymes known (RluA, RluC, RluD and TruC), of which staphylococci contain only three homologues: SAUPAN003179000, SAUPAN003477000, and SAUPAN004783000. All members contain the same XXHRLD consensus active site sequence and act on different RNA substrates to convert uridines into pseudouridines. SAUPAN003477000 can be unambiguously assigned as "rluD" due to its N-terminal, C-terminal and active site homology to E. coli RluD. The remaining staphylococcal RluA-like ΨS enzymes contain an N-terminal S4-like domain that is absent in E. coli RluA. After removing the S4-like domain, SAUPAN004783000 can be unambiguously assigned as "rluA" due to its truncated N-terminal, C-terminal and active site homology to E. coli RluA. Likewise, N-truncated SAUPAN003179000 aligns most closely with E. coli TruC. Based on the precedent that firmicutes contain only five Ψ residues in 23S rRNA, it is highly likely that staphylococci lack RluC enzymatic activity consistent with the functional assignments above. Therefore, 23S rRNA uridines at positions 955, 2504, and 2580 (E. coli numbering; 999, 2531, and 2607 by S. aureus numbering) are likely to remain uridines.
⊟Orthologs[edit | edit source]
⊟Genome Viewer[edit | edit source]
| COL | |
| N315 | |
| NCTC8325 | |
| Newman | |
| USA300_FPR3757 |
⊟Alignments[edit | edit source]
- alignment of orthologues: CLUSTAL format alignment by MAFFT L-INS-i (v7.307)
COL METYEFNITDKEQTGMRVDKLLPELNNDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLND
N315 METYEFNITDKEQTGMRVDKLLPELNNDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLND
NCTC8325 METYEFNITDKEQTGMRVDKLLPELNNDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLND
Newman METYEFNITDKEQTGMRVDKLLPELNNDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLND
USA300_FPR3757 METYEFNITDKEQTGMRVDKLLPELNNDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLND
************************************************************
COL HIVVTEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQI
N315 HIVVTEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQI
NCTC8325 HIVVTEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQI
Newman HIVVTEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQI
USA300_FPR3757 HIVVTEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQI
************************************************************
COL KNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIP
N315 KNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIP
NCTC8325 KNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIP
Newman KNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIP
USA300_FPR3757 KNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIP
************************************************************
COL HDYGTIDAPIGRNKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVH
N315 HDYGTIDAPIGRNKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVH
NCTC8325 HDYGTIDAPIGRNKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVH
Newman HDYGTIDAPIGRNKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVH
USA300_FPR3757 HDYGTIDAPIGRNKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVH
************************************************************
COL MKYIGFPLVGDPKYGPKKTLDIGGQALHAGLIGFEHPVTGEYIERHAELPQDFEDLLDTI
N315 MKYIGFPLVGDPKYGPKKTLDIGGQALHAGLIGFEHPVTGEYIERHAELPQDFEDLLDTI
NCTC8325 MKYIGFPLVGDPKYGPKKTLDIGGQALHAGLIGFEHPVTGEYIERHAELPQDFEDLLDTI
Newman MKYIGFPLVGDPKYGPKKTLDIGGQALHAGLIGFEHPVTGEYIERHAELPQDFEDLLDTI
USA300_FPR3757 MKYIGFPLVGDPKYGPKKTLDIGGQALHAGLIGFEHPVTSEYIERHAELPQDFEDLLDTI
***************************************.********************
COL RKRDA
N315 RKRDA
NCTC8325 RKRDA
Newman RKRDA
USA300_FPR3757 RKRDA
*****
- ↑ James Ofengand
Ribosomal RNA pseudouridines and pseudouridine synthases.
FEBS Lett: 2002, 514(1);17-25
[PubMed:11904174] [WorldCat.org] [DOI] (P p)Tomoko Hamma, Adrian R Ferré-D'Amaré
Pseudouridine synthases.
Chem Biol: 2006, 13(11);1125-35
[PubMed:17113994] [WorldCat.org] [DOI] (P p)Adrián González-López, Daniel S D Larsson, Ravi Kiran Koripella, Brett N Cain, Martin Garcia Chavez, Paul J Hergenrother, Suparna Sanyal, Maria Selmer
Structures of the Staphylococcus aureus ribosome inhibited by fusidic acid and fusidic acid cyclopentane.
Sci Rep: 2024, 14(1);14253
[PubMed:38902339] [WorldCat.org] [DOI] (I e)