Modomics - A Database of RNA Modifications

ID Card:

Full name:	tRNA pseudouridine(55) synthase
Synonym:	YhbA
GI:	42560511
Orf:	yhbA, b3166
COG:	COG0130
UniProt:	P60340
Structures:	\| 1K8W \| 1R3F \| 1R3E \| 1SGV \| 1ZL3 \|
Alpha Fold Predicted Structure:	AF-P60340-F1
Enzyme type:	pseudouridine synthase
Position of modification - modification:	t:55 - Y

PDB Structures:

1K8W

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Pseudouridine (Psi) synthases catalyze the isomerization of specific uridines in cellular RNAs to pseudouridines and may function as RNA chaperones. TruB is responsible for the Psi residue present in the T loops of virtually all tRNAs. The close homolog Cbf5/dyskerin is the catalytic subunit of box H/ACA snoRNPs. These carry out the pseudouridylation of eukaryotic rRNA and snRNAs. The 1.85 A resolution structure of TruB bound to RNA reveals that this enzyme recognizes the preformed three-dimensional structure of the T loop, primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA. Structural comparisons with TruB demonstrate that all Psi synthases are descended from a common molecular ancestor.

Download RCSB-PDB Structures:

Pdb Files	1K8W.pdb 1R3E.pdb 1R3F.pdb 1SGV.pdb 1ZL3.pdb
Pdbx/mmCIF Files	1K8W.cif 1R3E.cif 1R3F.cif 1SGV.cif 1ZL3.cif

Protein sequence:

MSRPRRRGRDINGVLLLDKPQGMSSNDALQKVKRIYNANRAGHTGALDPLATGMLPICLGEATKFSQYLLDSDKRYRVIARLGQRTDTSDADGQIVEERPVTFSAEQLAAALDTFRGDIEQIPSMYSALKYQGKKLYEYARQGIEVPREARPITVYELLFIRHEGNELELEIHCSKGTYIRTIIDDLGEKLGCGAHVIYLRRLAVSKYPVERMVTLEHLRELVEQAEQQDIPAAELLDPLLMPMDSPASDYPVVNLPLTSSVYFKNGNPVRTSGAPLEGLVRVTEGENGKFIGMGEIDDEGRVAPRRLVVEYPA

Comments:

Five pseudo (Y)-uridine synthases are conserved across all three life domains, including eukarya, bacteria, and archaea. In E.coli, these are named RluA, RsuA, TruA, TruB, and TruD. These families share poor sequence similarity. Nonetheless, these families share a core with a common fold and a conserved active cleft. This fold consists of an eight-stranded mixed beta-sheet with several helices and loops flanking the catalytic a cleft that bisects the sheet. Each of these families carries an essential aspartate residue that is catalytically active. This is the only residue that is absolutely conserved in all the Y-synthases. Depending on the enzyme, each core is additionally decorated with several secondary structural elements ( Hamma et al. 2006). TruB is responsible for synthesis of pseudouridine from uracil-55 in E.coli tRNAs ( Del Campo et al. 2001). The catalytically conserved aspartate is in position 48 (Asp48) .

Reaction	Substrate	SubstrateType	Position	(Anti)Codon	Modified (Anti)Codon	Transcript Name	Transcript Region	Cellular Localization	References
U:Y	RNA	tRNA	55	All tRNA isoacceptors	All tRNA isoacceptors			Prokaryotic Cytosol	11720289
U:Y	RNA	tRNA	55	VGC	VGC	tRNA^Ala_VGC	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GGC	GGC	tRNA^Ala_GGC	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	ICG	ICG	tRNA^Arg_ICG	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CCG	CCG	tRNA^Arg_CCG	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	UCU	UCU	tRNA^Arg_UCU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GUU	GUU	tRNA^Asn_GUU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	EUC	EUC	tRNA^Asp_EUC	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GCA	GCA	tRNA^Cys_GCA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	UUG	UUG	tRNA^Gln_UUG	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CUG	CUG	tRNA^Gln_CUG	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	SUC	SUC	tRNA^Glu_SUC	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CCC	CCC	tRNA^Gly_CCC	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	{CC	{CC	tRNA^Gly_{CC	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GCC	GCC	tRNA^Gly_GCC	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GUG	GUG	tRNA^His_GUG	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GAU	GAU	tRNA^Ile_GAU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CAU	CAU	tRNA^Ile_CAU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CAG	CAG	tRNA^Leu_CAG	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GAG	GAG	tRNA^Leu_GAG	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	)AA	)AA	tRNA^Leu_)AA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	BAA	BAA	tRNA^Leu_BAA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	SUU	SUU	tRNA^Lys_SUU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	MAU	MAU	tRNA^Met_MAU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GAA	GAA	tRNA^Phe_GAA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CGG	CGG	tRNA^Pro_CGG	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	UGA	UGA	tRNA^Ser_UGA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CGA	CGA	tRNA^Ser_CGA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GCU	GCU	tRNA^Ser_GCU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GGA	GGA	tRNA^Ser_GGA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GGU	GGU	tRNA^Thr_GGU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GGU	GGU	tRNA^Thr_GGU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CCA	CCA	tRNA^Trp_CCA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	QUA	QUA	tRNA^Tyr_QUA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	QUA	QUA	tRNA^Tyr_QUA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	VAC	VAC	tRNA^Val_VAC	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GAC	GAC	tRNA^Val_GAC	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GAC	GAC	tRNA^Val_GAC	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CAU	CAU	tRNA^Ini_CAU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CAU	CAU	tRNA^Ini_CAU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	{UC	{UC	tRNA^Glu_{UC	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	UAG	UAG	tRNA^Leu_UAG	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	UGU	UGU	tRNA^Thr_UGU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CAU	CAU	tRNA^Val_CAU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	U;U	U;U	tRNA^Thr_U;U	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	U;U	U;U	tRNA^Thr_U;U	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GAA	GAA	tRNA^Phe_GAA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GAA	GAA	tRNA^Phe_GAA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CAU	CAU	tRNA^Ile_CAU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CAU	CAU	tRNA^Ile_CAU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CAU	CAU	tRNA^Ile_CAU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CAU	CAU	tRNA^Ile_CAU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CAU	CAU	tRNA^Ile_CAU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CAU	CAU	tRNA^Ile_CAU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CAU	CAU	tRNA^Ile_CAU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	AUA	AUA	tRNA^Tyr_AUA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	AUA	AUA	tRNA^Tyr_AUA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	#AA	#AA	tRNA^Phe_#AA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	#AA	#AA	tRNA^Phe_#AA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	GAA	GAA	tRNA^Phe_GAA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	UUU	UUU	tRNA^Lys_UUU	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CCA	CCA	tRNA^Trp_CCA	TΨC-loop	Prokaryotic Cytosol
U:Y	RNA	tRNA	55	CAU	CAU	tRNA^Ini_CAU	TΨC-loop	Prokaryotic Cytosol

Alpha Fold Predicted Structure:

Clear Selection and Reset Camera

Protein sequence:

M S R P R R R G R D I N G V L L L D K P Q G M S S N D A L Q K V K R I Y N A N R A G H T G A L D P L A T G M L P I C L G E A T K F S Q Y L L D S D K R Y R V I A R L G Q R T D T S D A D G Q I V E E R P V T F S A E Q L A A A L D T F R G D I E Q I P S M Y S A L K Y Q G K K L Y E Y A R Q G I E V P R E A R P I T V Y E L L F I R H E G N E L E L E I H C S K G T Y I R T I I D D L G E K L G C G A H V I Y L R R L A V S K Y P V E R M V T L E H L R E L V E Q A E Q Q D I P A A E L L D P L L M P M D S P A S D Y P V V N L P L T S S V Y F K N G N P V R T S G A P L E G L V R V T E G E N G K F I G M G E I D D E G R V A P R R L V V E Y P A

Secondary Structure Alphabet

G: 3-turn helix (3₁₀helix)
H: α-helix
I: 𝝅-helix (5 - turn helix)
T: Hydrogen Bonded Turn
B: β-sheet
S: Bend
C: Coil (residues not present in any of the above conformations)
N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files	AF-P60340-F1.pdb
Alpha Fold Pdbx/mmCIF Files	AF-P60340-F1.cif
DSSP Secondary Structures	P60340.dssp

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	-
Deletion of the Escherichia coli pseudouridine synthase gene truB blocks formation of pseudouridine 55 in tRNA in vivo, does not affect exponential growth, but confers a strong selective disadvantage in competition with wild-type cells.	Gutgsell N, Englund N, Niu L, Kaya Y, Lane BG, Ofengand J	RNA	[details]	11142385	-
Pre-steady-state kinetic analysis of the three Escherichia coli pseudouridine synthases TruB, TruA, and RluA reveals uniformly slow catalysis.	Wright JR, Keffer-Wilkes LC, Dobing SR, Kothe U	RNA	[details]	21998096	-
An arginine-aspartate network in the active site of bacterial TruB is critical for catalyzing pseudouridine formation.	Friedt J, Leavens FM, Mercier E, Wieden HJ, Kothe U...	Nucleic Acids Res	[details]	24371284	-