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Information on EC 5.4.99.25 - tRNA pseudouridine55 synthase and Organism(s) Methanocaldococcus jannaschii and UniProt Accession Q60346
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5.4.99.25 tRNA pseudouridine55 synthaseIUBMB Comments
Pseudouridine synthase TruB from Escherichia coli specifically modifies uridine55 in tRNA molecules . The bifunctional archaeal enzyme also catalyses the pseudouridylation of uridine54 . It is not known whether the enzyme from Escherichia coli can also act on position 54 in vitro, since this position is occupied in Escherichia coli tRNAs by thymine.
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Word Map
- 5.4.99.25
- synthases
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pseudouridylation
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anticodon
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rna-guided
- 5-fluorouridine
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srnps
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thumb
- snornas
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eukaryal
The taxonomic range for the selected organisms is: Methanocaldococcus jannaschii
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
pus10, acbf5, psi synthase, pseudouridine synthase trub, pseudouridine 55 synthase, trna pseudouridine synthase, psi55s, ynl292w, trna:pseudouridine-55 synthase, rna pseudouridine synthase trub, 
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topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
additional information
cf. tRNA pseudouridine54 synthase, EC 5.4.99
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
tRNA uridine55 = tRNA pseudouridine55
the mechanism of uridine55 recognition by Cbf5 and the bacterial TruB are different
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SYSTEMATIC NAME
IUBMB Comments
tRNA-uridine55 uracil mutase
Pseudouridine synthase TruB from Escherichia coli specifically modifies uridine55 in tRNA molecules [1]. The bifunctional archaeal enzyme also catalyses the pseudouridylation of uridine54 [6]. It is not known whether the enzyme from Escherichia coli can also act on position 54 in vitro, since this position is occupied in Escherichia coli tRNAs by thymine.
CAS REGISTRY NUMBER
COMMENTARY
430429-15-5
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61506-89-6
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
tRNATrp uridine55
tRNATrp pseudouridine55
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tRNATrp containing or lacking 3'-CCA. aCbf5 and aGar1 together can function as a tRNA Psi55 synthase in a guide RNA-independent manner. This activity is enhanced by aNop10, but not by L7Ae. The aCbf5 alone can also produce Psi55 in tRNAs that contain the canonical 3'-CCA sequence and this activity is stimulated by aGar1. tRNAs lacking 3'-CCA can be modified only by the aCbf5-aGar1 complex. The presence of conserved C (or U) and A at tRNA positions 56 and 58, respectively, is not essential for aCbf5-mediated Psi55 formation
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?
tRNA uridine55
tRNA pseudouridine55
the enzyme also exhibits tRNA pseudouridine54 synthase activity. The forefinger loop (reminiscent of that of RluA) and an Arg and a Tyr residue of archaeal Pus10 as critical determinants for its tRNA pseudouridine54 synthase, but not for its tRNA pseudouridine55 activity. A Leu residue, in addition to the catalytic Asp, is essential for both activities. Archaeal Pus10 proteins must use a different mechanism of recognition for tRNA pseudouridine55 than for the recognition of pseudouridine54. It is proposed that archaeal Pus10 uses two distinct mechanisms for substrate uridine recognition and binding. No mutation mutation is detected that affects only tRNA pseudouridine54 synthase activity, both mechanisms for archaeal Pus10 activities must share some common features
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tRNA uridine55
tRNA pseudouridine55
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aCbf5 and aGar1 together can function as a tRNA pseudouridine55 synthase in a guide RNA-independent manner. This activity is enhanced by aNop10, but not by L7Ae. The aCbf5 alone can also produce pseudouridine55 in tRNAs that contain the canonical 3-CCA sequence and this activity is stimulated by aGar1. The presence of C (or U) and A at tRNA position 56 and 58, respectively are not essential for Cbf5-mediated PSI55 formation. Variation in the structure of the anticodon arm of the tRNA does not affect the PSI55 synthase activity
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?
tRNA uridine55
tRNA pseudouridine55
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the bifunctional enzyme can act as synthase for both tRNA pseudouridine54 and pseudouridine55. The two modifications seem to occur independently. Unlike bacterial TruB and yeast Pus4, archaeal Pus10 does not require a U54*A58 reverse Hoogstein base pair and pyrimidine at position 56 to convert tRNA uridine55 to pseudouridine55. Although the T(PSI)PSI-arm of tRNA is a good substrate for both pseudouridine54 and pseudouridine55 synthesis by Mj-Pus10, the production of pseudouridine55 is more efficient than that of pseudouridine54 in this substrate. This contrasts with full-size tRNA substrates, where syntheses of pseudourines appear to be equally efficient
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
aGar1 protein
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the aCbf5 alone can produce pseudouridine55 in tRNAs that contain the canonical 3-CCA sequence. This activity is stimulated by aGar1
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aNop10 protein
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aCbf5 and aGar1 together can function as a tRNA pseudouridine55 synthase in a guide RNA-independent manner. This activity is enhanced by aNop10, but not by L7Ae
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protein aGar1
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aCbf5 alone can also produce Y55 in tRNAs that contain the canonical 3'-CCA sequence and this activity is stimulated by aGar1
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protein aNOP10
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aCbf5 and aGar1 together can function as a tRNA Y55 synthase in a guide RNA-independent manner. This activity is enhanced by aNop10, but not by L7Ae
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
in archaea, pseudouridine (Psi) synthase Pus10 modifies uridine (U) to Psi at positions 54 and 55 of tRNA. Pus10 is not found in bacteria, where modifications at those two positions are carried out by TrmA (U54 to m5U54) and TruB (U55 to Psi55). Many eukaryotes have an apparent redundancy, their genomes contain orthologues of archaeal Pus10 and bacterial TrmA and TruB. Eukaryal Pus10 genes share a conserved catalytic domain with archaeal Pus10 genes. Pus10 is found in earlier evolutionary branches of fungi (such as chytrid Batrachochytrium) but is absent in all dikaryon fungi surveyed (Ascomycetes and Basidiomycetes). Examination of 116 archaeal and eukaryotic Pus10 protein sequences reveals that Pus10 exists as a single copy gene in all the surveyed genomes despite ancestral whole genome duplications had occurred. Functional redundancy result in gene loss or neofunctionalization in different evolutionary lineages. The enzyme is a member of the pseudouridine synthase superfamily with a similar three-dimensional structure and a conserved catalytic Asp. In the catalytic region, five amino acids (Asp275, Tyr339, Ile412, Lys413, Leu440 in Methanocalcoccus jannaschii) are conserved throughout all pseudouridine synthase families
additional information
homology modeling and structural superimposition using the crystal structure of Homo sapiens enzyme Pus10, PDB ID 2V9K, as a template, overview
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
homology modeling and structural superimposition, overview
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C106A/C109A
decrease in tRNA pseudouridine54 synthase activity, no decrease in tRNA pseudouridine55 synthase activity
D275A
the mutant shows no tRNA pseudouridine54 synthase activity and no tRNA pseudouridine55 synthase activity
D277A
decrease in tRNA pseudouridine54 synthase activity and low decrease in tRNA pseudouridine55 synthase activity
H376A/R377A
decrease in tRNA pseudouridine54 synthase activity and in tRNA pseudouridine55 synthase activity
I412A
decrease in tRNA pseudouridine54 synthase activity and in tRNA pseudouridine55 synthase activity
K413A
decrease in tRNA pseudouridine54 synthase activity and in tRNA pseudouridine55 synthase activity
L440A
the mutant shows no tRNA pseudouridine54 synthase activity and no tRNA pseudouridine55 synthase activity
R273A
decrease in tRNA pseudouridine54 synthase activity and in tRNA pseudouridine55 synthase activity
Y339A
the mutant shows no tRNA pseudouridine54 synthase activity and no tRNA pseudouridine55 synthase activity
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
wild-type and mutant enzymes, expression in Escherichia coli. Wild-type enzyme can produce both pseudouridine54 and pseudouridine55 in Escherichia coli tRNAs
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Gurha, P.; Gupta, R.
Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA
RNA
14
2521-2527
2008
Methanocaldococcus jannaschii, Pyrococcus furiosus
Gurha, P.; Joardar, A.; Chaurasia, P.; Gupta, R.
Differential roles of archaeal box H/ACA proteins in guide RNA-dependent and independent pseudouridine formation
RNA Biol.
4
101-109
2007
Methanocaldococcus jannaschii
Joardar, A.; Jana, S.; Fitzek, E.; Gurha, P.; Majumder, M.; Chatterjee K, Geisler M, Gupta R.
Role of forefinger and thumb loops in production of Psi54 and Psi55 in tRNAs by archaeal Pus10
RNA
19
1279-1294
2013
Methanocaldococcus jannaschii (Q60346), Methanocaldococcus jannaschii DSM 2661 (Q60346)
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