Modomics - A Database of RNA Modifications

Full name:	Ribosomal large subunit pseudouridine synthase D
Synonym:	YfiI, SfhB
GI:	2507541
Orf:	yfiI, b2594
COG:	COG0564
UniProt:	P33643
Structures:	\| 1PRZ \| 1QYU \| 1V9F \| 2IST \|
Complex:
Enzyme type:	pseudouridine synthase
Position of modification - modification:	l:1911(1911) - Y l:1917(1917) - Y l:1915(1915) - Y

Comments:

RluD makes pseudouridines at positions 1911, 1915, and 1917 in the loop of hairpin 69 in 23S RNA (Domain IV). These are the most conserved (and probably best studied) ribosomal pseudouridines known in Bacteria. RluD lacking cells exhibit growth defects and abnormal ribosome biogenesis. Moreover, the interactions around the Y1917 was shown to be critical for a proper interaction of helix 69 with release factors. When tested in vitro, recombinant RluD works best at low Mg concentrations. While in vivo, naturally occurring RluD modifies all three sites, U1911 has never been modified in vitro, even after conditions optimisation. RluD molecule consists of two subdomains, a catalytic subdomain and C-terminal subdomain with the RNA-binding cleft formed by loops extending from the catalytic subdomain. The catalytic subdomain of RluD has a similar fold as TruA, TruB and RsuA, with the location of the RNA-binding cleft, active-site and conserved, catalytic Asp residue 169 superposing in all four structures. The RluD N-terminal S4 domain is connected to the rest of the protein by a flexible linker. RluD is among the best studied RNA pseudouridine synthases.

Protein sequence:

MAQRVQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPR
DLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA
VHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAP
IPQDMVELIEVMRADFEEHKDEVDWL

Enzymatic activities:

Reaction	Substrate	Type	Position
U:Y	rRNA (r)	LSU/23S/prokaryotic cytosol	1911
U:Y	rRNA (r)	LSU/23S/prokaryotic cytosol	1915
U:Y	rRNA (r)	LSU/23S/prokaryotic cytosol	1917

Publications:

Title	Authors	Journal	Details	PubMed Id	DOI
A second function for pseudouridine synthases: A point mutant of RluD unable to form pseudouridines 1911, 1915, and 1917 in Escherichia coli 23S ribosomal RNA restores normal growth to an RluD-minus strain.	Gutgsell NS, Del Campo M, Raychaudhuri S, Ofengand J	RNA	[details]	11453071	-
The pseudouridine synthase RluD is required for normal ribosome assembly and function in Escherichia coli.	Gutgsell NS, Deutscher MP, Ofengand J	RNA	[details]	15928344	-
RluD, a highly conserved pseudouridine synthase, modifies 50S subunits more specifically and efficiently than free 23S rRNA.	Vaidyanathan PP, Deutscher MP, Malhotra A	RNA	[details]	17872507	-
Specificity and kinetics of 23S rRNA modification enzymes RlmH and RluD.	Ero R, Leppik M, Liiv A, Remme J	RNA	[details]	20817755	-
Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli.	Mizutani K, Machida Y, Unzai S, Park SY, Tame JR	Biochemistry	[details]	15078091	-
Crystal structure of the catalytic domain of RluD, the only rRNA pseudouridine synthase required for normal growth of Escherichia coli.	Del Campo M, Ofengand J, Malhotra A	RNA	[details]	14730022	-
Substrate specificity of the pseudouridine synthase RluD in Escherichia coli.	Leppik M, Peil L, Kipper K, Liiv A, Remme J	FEBS J	[details]	17937767	-
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.	Sivaraman J, Iannuzzi P, Cygler M, Matte A	J Mol Biol	[details]	14659742	-