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Information on EC 5.4.99.21 - 23S rRNA pseudouridine2604 synthase and Organism(s) Escherichia coli and UniProt Accession P32684

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EC Tree
     5 Isomerases
         5.4 Intramolecular transferases
             5.4.99 Transferring other groups
                5.4.99.21 23S rRNA pseudouridine2604 synthase
IUBMB Comments
The enzyme is not completely specific for uridine2604 and can, to a small extent, also react with uridine2605 .
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This record set is specific for:
Escherichia coli
UNIPROT: P32684
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The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
23S rRNA uridine2604
=
23S rRNA pseudouridine2604
Synonyms
RluF, YjbC, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
23S rRNA uridine2604 = 23S rRNA pseudouridine2604
show the reaction diagram
the substrate of RluF undergoes radical structural rearrangements upon binding. The RluF target base lies in an RNA stem rather than in a flexible loop and the substrate conformational change requires disruption of multiple base pairs. This energetically costly process is driven by interactions of the RNA with the protein, a mechanism of RluF is proposed
SYSTEMATIC NAME
IUBMB Comments
23S rRNA-uridine2604 uracil mutase
The enzyme is not completely specific for uridine2604 and can, to a small extent, also react with uridine2605 [1].
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
23S rRNA uridine2604
23S rRNA pseudouridine2604
show the reaction diagram
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
pseudouridine2604 is absent in the RluF-deletion strain
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of Escherichia coli RluF in a complex with a 22-mer RNA substrate analog identical in sequence to the substrate rRNA stem-loop, except with the target U2604 substituted by 5-fluorouridine to block a late step in catalysis. The structure shows that association with RluF induces a rearrangement of the RNA stem-loop, resulting in a frame-shift in base pairing. A bulge in the RNA is induced to fold into the stem, causing the RNA 3' to the bulge to translate by 1nt, thereby flipping out U2604 into the active site
hanging-drop vapor-diffusion method, domain architecture and crystal structure of the catalytic domain of RluF at 2.6 A resolution. Limited proteolysis, mass spectrometry and N-terminal sequencing indicate that RluF has a distinct domain architecture, with the catalytic domain flanked at the N and C termini by additional domains connected to it by flexible linkers. The structure of the catalytic domain of RluF is similar to those of RsuA and TruB. Structural comparison of RluF with its closest structural homologues, RsuA and TruB, suggests possible functional roles for the N-terminal and C-terminal domains of RluF
hanging-drop vapor-diffusion method, X-ray crystal structure of RluF bound to the isolated stem–loop, in which uridine2604 is substituted by 5-fluorouridine to prevent catalytic turnover
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D107N
inactive mutant enzyme
D107T
inactive mutant enzyme
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
full-length RluF and N-terminal, 65-residue-truncated RulF (DELTARulF)
using Ni-NTA chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli as a His-tagged fusion protein
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Sunita, S.; Zhenxing, H.; Swaathi, J.; Cygler, M.; Matte, A.; Sivaraman, J.
Domain organization and crystal structure of the catalytic domain of E.coli RluF, a pseudouridine synthase that acts on 23S rRNA
J. Mol. Biol.
359
998-1009
2006
Escherichia coli (P32684)
Manually annotated by BRENDA team
Alian, A.; DeGiovanni, A.; Griner, S.L.; Finer-Moore, J.S.; Stroud, R.M.
Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome
J. Mol. Biol.
388
785-800
2009
Escherichia coli (P32684)
Manually annotated by BRENDA team
Del Campo, M.; Kaya, Y.; Ofengand, J.
Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli
RNA
7
1603-1615
2001
Escherichia coli (P32684)
Manually annotated by BRENDA team
Czudnochowski, N.; Ashley, G.W.; Santi, D.V.; Alian, A.; Finer-Moore, J.; Stroud, R.M.
The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs
Nucleic Acids Res.
42
2037-2048
2014
Escherichia coli (P32684)
Manually annotated by BRENDA team