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Information on EC 5.4.99.27 - tRNA pseudouridine13 synthase and Organism(s) Escherichia coli and UniProt Accession Q57261

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     5 Isomerases
         5.4 Intramolecular transferases
             5.4.99 Transferring other groups
                5.4.99.27 tRNA pseudouridine13 synthase
IUBMB Comments
Pseudouridine synthase TruD from Escherichia coli specifically acts on uridine13 in tRNA [2,3]. The Pus7 protein from Saccharomyces cerevisiae is a multisite-multisubstrate pseudouridine synthase that is able to modify uridine13 in several yeast tRNAs, uridine35 in the pre-tRNATyr, uridine35 in U2 small nuclear RNA, and uridine50 in 5S rRNA .
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This record set is specific for:
Escherichia coli
UNIPROT: Q57261
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Word Map
The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Reaction Schemes
tRNA uridine13
=
tRNA pseudouridine13
Synonyms
pus7p, pus7 protein, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tRNA PSI13 synthase
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
tRNA uridine13 = tRNA pseudouridine13
show the reaction diagram
a strictly conserved glutamate near the active site in TruD is likely to act as a general base for the proton abstraction at C5 of the uridine base
SYSTEMATIC NAME
IUBMB Comments
tRNA-uridine13 uracil mutase
Pseudouridine synthase TruD from Escherichia coli specifically acts on uridine13 in tRNA [2,3]. The Pus7 protein from Saccharomyces cerevisiae is a multisite-multisubstrate pseudouridine synthase that is able to modify uridine13 in several yeast tRNAs, uridine35 in the pre-tRNATyr, uridine35 in U2 small nuclear RNA, and uridine50 in 5S rRNA [5].
CAS REGISTRY NUMBER
COMMENTARY hide
430429-15-5
-
61506-89-6
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
tRNA uridine13
tRNA pseudouridine13
show the reaction diagram
-
-
-
?
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00038
tRNA uridine13
-
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00097
tRNA uridine13
-
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.255
tRNA uridine13
-
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
TruD folds into a V-shaped molecule with a catalytic domain that is structurally very similar to the catalytic modules of the other known pseudouridine synthases despite its lack of sequence homology and likely arose by divergent evolution
malfunction
deletion of the ygbO gene causes the loss of tRNAGlu pseudouridine13 and plasmid-borne restoration of the structural gene restores pseudouridine13. Growth competition does not show any effect of the deletion
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
39100
x * 39100, calculated from sequence, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 39100, calculated from sequence, SDS-PAGE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of Escherichia coli TruD at 2.0 A resolution. The structure reveals an overall V-shaped molecule with an RNA binding cleft formed between two domains: a catalytic domain and an insertion domain
crystals of TruD are grown at room temperature by the hanging drop vapor diffusion method. TruD folds into a V-shaped molecule with a catalytic domain that is structurally very similar to the catalytic modules of the other known pseudouridine synthases despite its lack of sequence homology and likely arose by divergent evolution
hanging drop vapor diffusion method, 2.2 A resolution structure. TruD reveals a U-shaped molecule with a catalytic domain that superimposes closely on that of other pseudouridine synthases
sitting-drop vapour-diffusion method, crystals diffract to a minimum Bragg spacing of 2.4 A and belong to space group P212121, with unit-cell parameters a = 63.4, b = 108.6, c = 111.7 A
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E31D
27% of wild-type activity
E31Q
no activity
E31Q/F131Y
no activity
F131Y
68% of wild-type activity
K79L/F131Y
no activity
K79L/N129K/F131Y
no activity
K79R
10% of wild-type activity
N129K
no activity
Q87E
29% of wild-type activity
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ericsson, U.B.; Andersson, M.E.; Engvall, B.; Nordlund, P.; Hallberg, B.M.
Expression, purification, crystallization and preliminary diffraction studies of the tRNA pseudouridine synthase TruD from Escherichia coli
Acta Crystallogr. Sect. D
60
775-776
2004
Escherichia coli (Q57261)
Manually annotated by BRENDA team
Kaya, Y.; Del Campo, M.; Ofengand, J.; Malhotra, A.
Crystal structure of TruD, a novel pseudouridine synthase with a new protein fold
J. Biol. Chem.
279
18107-18110
2004
Escherichia coli (Q57261)
Manually annotated by BRENDA team
Ericsson, U.B.; Nordlund, P.; Hallberg, B.M.
X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold
FEBS Lett.
565
59-64
2004
Escherichia coli (Q57261)
Manually annotated by BRENDA team
Hoang, C.; Ferre-D'Amare, A.R.
Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold
RNA
10
1026-1033
2004
Escherichia coli (Q57261), Escherichia coli
Manually annotated by BRENDA team
Chan, C.M.; Huang, R.H.
Enzymatic characterization and mutational studies of TruD--the fifth family of pseudouridine synthases
Arch. Biochem. Biophys.
489
15-19
2009
Escherichia coli (Q57261)
Manually annotated by BRENDA team
Kaya, Y.; Ofengand, J.
A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya
RNA
9
711-721
2003
Escherichia coli (Q57261)
Manually annotated by BRENDA team