Modomics - A Database of RNA Modifications

Full name:	Ribosomal large subunit pseudouridine synthase F
Synonym:	YjbC
GI:	418534
Orf:	yjbC, b4022
COG:	COG1187
UniProt:	P32684
Structures:	\| 2GML \| 3DH3 \|
Complex:
Enzyme type:	pseudouridine synthase
Position of modification - modification:	l:2604(2604) - Y

Comments:

RluF modifies U2604 in a stem-loop (helix 93 of the Peptidyl transferase Center on Domain V) of 23S RNA, while its homologue, RluB, modifies the adjacent base, U2605. Both uridines are in the same RNA stem, separated by only 4 A. The RNA stem-loop is bound to a conserved binding groove in the catalytic domain. A base from a bulge in the stem, A2602, folds into the stem, forcing one strand of the RNA stem to translate by one position and thus positioning U2604 to flip into the active site. The structure of the catalytic domain of RluF is similar to those of RsuA and TruB. RluF is a member of the RsuA family of pseudouridine synthases, along with RluB and RluE (but not TruB), present in all kingdoms of life.

Protein sequence:

MLPDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEPREAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRV
FPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEV
KKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR

Enzymatic activities:

Reaction	Substrate	Type	Position
U:Y	rRNA (r)	LSU/23S/prokaryotic cytosol	2604

Publications:

Title	Authors	Journal	Details	PubMed Id	DOI
Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli.	Del Campo M, Kaya Y, Ofengand J	RNA	[details]	11720289	-
Domain organization and crystal structure of the catalytic domain of E.coli RluF, a pseudouridine synthase that acts on 23S rRNA.	Sunita S, Zhenxing H, Swaathi J, Cygler M, Matte A, Sivaraman J	J Mol Biol	[details]	16712869	-
Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.	Alian A, DeGiovanni A, Griner SL, Finer-Moore JS, Stroud RM	J Mol Biol	[details]	19298824	-