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Information on EC 2.7.7.87 - L-threonylcarbamoyladenylate synthase
for references in articles please use BRENDA:EC2.7.7.87
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EC Tree 2 Transferases
2.7 Transferring phosphorus-containing groups
2.7.7 Nucleotidyltransferases
2.7.7.87 L-threonylcarbamoyladenylate synthase
IUBMB Comments
The enzyme is involved in the synthesis of N6-threonylcarbamoyladenosine37 in tRNAs, with the anticodon NNU, i.e. tRNAIle, tRNAThr, tRNAAsn, tRNALys, tRNASer and tRNAArg .
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
showSynonyms
sua5 protein, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
SUA5
YrdC
YwlC
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
L-threonine + ATP + HCO3- = L-threonylcarbamoyladenylate + diphosphate + H2O
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
BRENDA
MetaCyc
N6-L-threonylcarbamoyladenosine37-modified tRNA biosynthesis
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SYSTEMATIC NAME
IUBMB Comments
ATP:L-threonyl,bicarbonate adenylyltransferase
The enzyme is involved in the synthesis of N6-threonylcarbamoyladenosine37 in tRNAs, with the anticodon NNU, i.e. tRNAIle, tRNAThr, tRNAAsn, tRNALys, tRNASer and tRNAArg [6].
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
additional information
?
-
-
Substrates: t6A is a universally conserved tRNA modification found at position 37 in the anticodon loop of a subset of tRNA, structural studies predict an important role for t6A in translational fidelity
Products: -
Products: -
?
L-threonine + ATP + bicarbonate
L-threonylcarbamoyladenylate + diphosphate + H2O
-
Substrates: -
Products: threonylcarbamoyladenosine i.e. t6A
Products: threonylcarbamoyladenosine i.e. t6A
?
L-threonine + ATP + bicarbonate
L-threonylcarbamoyladenylate + diphosphate + H2O
Substrates: results indicate that the universally conserved YrdC family is involved in the biosynthesis of N6-threonylcarbamoyl adenosine
Products: threonylcarbamoyladenosine i.e. t6A
Products: threonylcarbamoyladenosine i.e. t6A
?
L-threonine + ATP + bicarbonate
L-threonylcarbamoyladenylate + diphosphate + H2O
-
Substrates: YrdC is an ATPase that binds L-threonine and tRNAs that respond to codons beginning with adenosine. The enzyme recognizes the heptadecamer anticodon stem and loop of tRNALysUUU
Products: -
Products: -
?
L-threonine + ATP + bicarbonate
L-threonylcarbamoyladenylate + diphosphate + H2O
-
Substrates: beside YrdC, proteins YgjD, YjeE and YeaZ are necessary and sufficient for t6A biosynthesis in vitro
Products: L-threonylcarbamoyladenylate i.e. t6A
Products: L-threonylcarbamoyladenylate i.e. t6A
?
L-threonine + ATP + bicarbonate
L-threonylcarbamoyladenylate + diphosphate + H2O
-
Substrates: PaSua5 and PaKEOPS together catalyse the biosynthesis of L-threonylcarbamoyladenylate i.e. t6A
Products: -
Products: -
?
L-threonine + ATP + bicarbonate
L-threonylcarbamoyladenylate + diphosphate + H2O
Substrates: results indicate that the universally conserved SUA5 family is involved in the biosynthesis of N6-threonylcarbamoyl adenosine
Products: threonylcarbamoyladenosine i.e. t6A
Products: threonylcarbamoyladenosine i.e. t6A
?
L-threonine + ATP + bicarbonate
L-threonylcarbamoyladenylate + diphosphate + H2O
-
Substrates: ScSua5 and ScKEOPS together catalyse the biosynthesis of L-threonylcarbamoyladenylate i.e. t6A
Products: -
Products: -
?
L-threonine + ATP + bicarbonate
L-threonylcarbamoyladenylate + diphosphate + H2O
-
Substrates: the combination of Qri7 and Sua5 is necessary and sufficient for L-threonylcarbamoyladenylate biosynthesis
Products: -
Products: -
?
L-threonine + ATP + bicarbonate
L-threonylcarbamoyladenylate + diphosphate + H2O
Substrates: determination of thermodynamic parameters of L-threonine, L-serine, ATP, ADP, AMP binding to Sua5 by ITC measurements
Products: -
Products: -
?
L-threonine + ATP + CO2
L-threonylcarbamoyl-AMP + diphosphate
Substrates: catalyzed by YwlC(TsaC)
Products: L-threonylcarbamoyl-AMP i.e. TC-AMP, isolated by HPLC and characterized by mass spectrometry and 1H-NMR
Products: L-threonylcarbamoyl-AMP i.e. TC-AMP, isolated by HPLC and characterized by mass spectrometry and 1H-NMR
?
L-threonine + ATP + CO2
L-threonylcarbamoyl-AMP + diphosphate
Substrates: catalyzed by YwlC(TsaC)
Products: L-threonylcarbamoyl-AMP i.e. TC-AMP, isolated by HPLC and characterized by mass spectrometry and 1H-NMR
Products: L-threonylcarbamoyl-AMP i.e. TC-AMP, isolated by HPLC and characterized by mass spectrometry and 1H-NMR
?
L-threonylcarbamoyl-AMP + tRNA
t6A37-tRNA
Substrates: catalyzed by YdiBCE(TsaEBD), a study of RNA substrate specificity shows that tRNA(Thr) and tRNA(Lys) are modified, whereas tRNA(Phe) is not modified
Products: -
Products: -
?
L-threonylcarbamoyl-AMP + tRNA
t6A37-tRNA
Substrates: catalyzed by YdiBCE(TsaEBD), a study of RNA substrate specificity shows that tRNA(Thr) and tRNA(Lys) are modified, whereas tRNA(Phe) is not modified
Products: -
Products: -
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
L-threonine + ATP + bicarbonate
L-threonylcarbamoyladenylate + diphosphate + H2O
-
Substrates: -
Products: threonylcarbamoyladenosine i.e. t6A
Products: threonylcarbamoyladenosine i.e. t6A
?
L-threonine + ATP + bicarbonate
L-threonylcarbamoyladenylate + diphosphate + H2O
Substrates: results indicate that the universally conserved YrdC family is involved in the biosynthesis of N6-threonylcarbamoyl adenosine
Products: threonylcarbamoyladenosine i.e. t6A
Products: threonylcarbamoyladenosine i.e. t6A
?
L-threonine + ATP + bicarbonate
L-threonylcarbamoyladenylate + diphosphate + H2O
-
Substrates: YrdC is an ATPase that binds L-threonine and tRNAs that respond to codons beginning with adenosine. The enzyme recognizes the heptadecamer anticodon stem and loop of tRNALysUUU
Products: -
Products: -
?
L-threonine + ATP + bicarbonate
L-threonylcarbamoyladenylate + diphosphate + H2O
Substrates: results indicate that the universally conserved SUA5 family is involved in the biosynthesis of N6-threonylcarbamoyl adenosine
Products: threonylcarbamoyladenosine i.e. t6A
Products: threonylcarbamoyladenosine i.e. t6A
?
L-threonine + ATP + CO2
L-threonylcarbamoyl-AMP + diphosphate
Substrates: catalyzed by YwlC(TsaC)
Products: L-threonylcarbamoyl-AMP i.e. TC-AMP, isolated by HPLC and characterized by mass spectrometry and 1H-NMR
Products: L-threonylcarbamoyl-AMP i.e. TC-AMP, isolated by HPLC and characterized by mass spectrometry and 1H-NMR
?
L-threonine + ATP + CO2
L-threonylcarbamoyl-AMP + diphosphate
Substrates: catalyzed by YwlC(TsaC)
Products: L-threonylcarbamoyl-AMP i.e. TC-AMP, isolated by HPLC and characterized by mass spectrometry and 1H-NMR
Products: L-threonylcarbamoyl-AMP i.e. TC-AMP, isolated by HPLC and characterized by mass spectrometry and 1H-NMR
?
L-threonylcarbamoyl-AMP + tRNA
t6A37-tRNA
Substrates: catalyzed by YdiBCE(TsaEBD), a study of RNA substrate specificity shows that tRNA(Thr) and tRNA(Lys) are modified, whereas tRNA(Phe) is not modified
Products: -
Products: -
?
L-threonylcarbamoyl-AMP + tRNA
t6A37-tRNA
Substrates: catalyzed by YdiBCE(TsaEBD), a study of RNA substrate specificity shows that tRNA(Thr) and tRNA(Lys) are modified, whereas tRNA(Phe) is not modified
Products: -
Products: -
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mn2+
Mn2+
-
stimulating effect, it increases the yield of the reaction to 38%
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00011
L-threonine
-
pH 8.0, temperature not specified in the publication
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Highest Expressing Human Cell Lines
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
-
the loss of SUA5 causes increased leaky scanning through AUG codons, +1 frameshifting, and nonsense suppression. In addition, the loss of SUA5 amplifies the 20S RNA virus found in Saccharomyces cerevisiae, possibly through an internal ribosome entry site-mediated mechanism
physiological function
physiological function
threonylcarbamoyladenosine is a universal modification found at position 37 of ANN decoding tRNAs, which imparts a unique structure to the anticodon loop enhancing its binding to ribosomes in vitro
physiological function
threonylcarbamoyladenosine is a universal modification found at position 37 of ANN decoding tRNAs, which imparts a unique structure to the anticodon loop enhancing its binding to ribosomes in vitro
physiological function
-
YrdC, with many of the properties of a putative threonylcarbamoyl transferase, most likely functions as a component of a heteromultimeric protein complex for threonylcarbamoyladenosine biosynthesis
physiological function
-
L-threonylcarbamoyladenylate is a modified nucleotide found in all tRNAs decoding codons starting with adenosine, its role is to facilitate codonanticodon pairing and to prevent frameshifting during protein synthesis
physiological function
-
L-threonylcarbamoyladenylate is a modified nucleotide found in all tRNAs decoding codons starting with adenosine, its role is to facilitate codonanticodon pairing and to prevent frameshifting during protein synthesis
physiological function
-
t6A is a universally conserved tRNA modification found at position 37 in the anticodon loop of a subset of tRNA, structural studies predict an important role for t6A in translational fidelity
physiological function
-
the eukaryotic L-threonylcarbamoyladenylate biosynthesis system functions first through Sua5, which generates threonylcarbamoyl-adenylate using its adenylation function and then secondly through Qri7, which binds to threonylcarbamoyl-adenylate to conjugate the threonyl-carbamoyl moiety onto directly bound tRNA substrates
physiological function
-
the Sua5 protein is essential for normal translational regulation in yeast
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
200000
-
recombinant PaKEOPS complex consisting of Kae1, Bud32, Cgi121 and Pcc1, gel filtration
38200
determined by analytical ultracentrifugation at 20°C and at 25°C
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
1 * 38200, analytical ultracentrifugation, Sulfolobus tokodaii Sua5 exists as a monomer in solution
additional information
-
fluorescence quenching data indicate that YrdC recognizes the RNA substrate in a sequence-dependent manner by directly interacting with certain bases
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystals grown at 30°C by sitting drop method, complexed with L-threonine and AMPPNP at 1.8 A resolution
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
attempts to purify the native forms of YdiC and YdiE by specific cleavage of the fusion proteins with thrombin or Factor Xa protease lead to multiple products, perhaps because the proteins are not completely stable in the cleavage reaction conditions
by Ni-NTA affinity chromatography to a purity of more than 95% by SDS-PAGE
-
gravity-flow chromatography on an Ni-NTA resin column, not associated with tRNAs when purified
-
gravity-flow chromatography on an Ni-NTA resin column, PaKEOPS complex co-purified with nucleic acids
-
yrdC protein purified by Ni-NTA affinity chromatography, dialyzed against phosphate-buffered saline and concentrated using a YM-3 Centriprep filter
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
a polycistronic sequence containing the genes encoding the PaKEOPS protein subunits Kae, Bud32, Cgi121 and Pcc1 synthesized and cloned into pET28(a) plasmid and transformed in Escherichia coli, Pcc1 fused to a hexa-histidine tag, PaSua5 cloned into pET26b
-
Escherichia coli BL21(DE3) cells transformed with a pET21 derivative (Novagen) vector containing the Escherichia coli yrdC gene
full length Sua5 expressed in Escherichia coli BL21 (DE3) CodonPlus cells harboring an N-terminal hexa-histidine tag
-
ScSua5 gene amplified by PCR using genomic DNA from Saccharomyces cerevisiae, fused to a hexa-histidine tag at its 3'-end and cloned into pET21d vector and transformed in Escherichia coli
-
SDS-PAGE, cloning of ywlC and ydiB as His6 N-fusion proteins and highly expression in Escherichia coli BL21(DE3), because of inclusion bodies construction of N-terminal thioredoxin (trxA) fusion proteins of ydiC and ydiE, which allow good expression and sufficient solubility for in vitro studies
Sulfolobus tokodaii Sua5 protein overexpressed in Escherichia coli
yrdC, yjeE and yeaZ genes from Escherichia coli expressed as N-terminal His6-fusion proteins, YgjD N-terminal as His6-SUMO fusion protein in Escherichia coli
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Lauhon, C.T.
Mechanism of N6-threonylcarbamoyladenonsine (t6A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP
Biochemistry
51
8950-8963
2012
Bacillus subtilis (P39153), Bacillus subtilis 168 (P39153)
brenda
El Yacoubi, B.; Lyons, B.; Cruz, Y.; Reddy, R.; Nordin, B.; Agnelli, F.; Williamson, J.R.; Schimmel, P.; Swairjo, M.A.; Crecy-Lagard, V.
The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA
Nucleic Acids Res.
37
2894-2909
2009
Saccharomyces cerevisiae (P32579), Escherichia coli (P45748)
brenda
Kuratani, M.; Kasai, T.; Akasaka, R.; Higashijima, K.; Terada, T.; Kigawa, T.; Shinkai, A.; Bessho, Y.; Yokoyama, S.
Crystal structure of Sulfolobus tokodaii Sua5 complexed with L-threonine and AMPPNP.
Proteins
79
2065-2075
2011
Sulfurisphaera tokodaii (Q970S6)
brenda
Harris, K.A.; Jones, V.; Bilbille, Y.; Swairjo, M.A.; Agris, P.F.
YrdC exhibits properties expected of a subunit for a tRNA threonylcarbamoyl transferase
RNA
17
1678-1687
2011
Escherichia coli
brenda
Deutsch, C.; El Yacoubi, B.; de Crecy-Lagard, V.; Iwata-Reuyl, D.
Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside
J. Biol. Chem.
287
13666-13673
2012
Escherichia coli
brenda
Lin, C.A.; Ellis, S.R.; True, H.L.
The Sua5 protein is essential for normal translational regulation in yeast
Mol. Cell. Biol.
30
354-363
2010
Saccharomyces cerevisiae
brenda
Perrochia, L.; Crozat, E.; Hecker, A.; Zhang, W.; Bareille, J.; Collinet, B.; van Tilbeurgh, H.; Forterre, P.; Basta, T.
In vitro biosynthesis of a universal t6A tRNA modification in Archaea and Eukarya
Nucleic Acids Res.
41
1953-1964
2013
Pyrococcus abyssi, Saccharomyces cerevisiae
brenda
Wan, L.C.K.; Mao, D.Y.L.; Neculai, D.; Strecker, J.; Chiovitti, D.; Kurinov, I.; Poda, G.; Thevakumaran, N.; Yuan, F.; Szilard, R.K.; Lissina, E.; Nislow, C.; Caudy, A.A.; Durocher, D.; Sicheri, F.
Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system
Nucleic Acids Res.
41
6332-6346
2013
Saccharomyces cerevisiae
brenda
Harris, K.A.; Shekhtman, A.; Agris, P.F.
Specific RNA-protein interactions detected with saturation transfer difference NMR
RNA Biol.
10
1307-1311
2013
Escherichia coli
brenda
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