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Information on EC 2.7.7.72 - CCA tRNA nucleotidyltransferase and Organism(s) Archaeoglobus fulgidus and UniProt Accession O28126

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EC Tree
IUBMB Comments
The acylation of all tRNAs with an amino acid occurs at the terminal ribose of a 3' CCA sequence. The CCA sequence is added to the tRNA precursor by stepwise nucleotide addition performed by a single enzyme that is ubiquitous in all living organisms. Although the enzyme has the option of releasing the product after each addition, it prefers to stay bound to the product and proceed with the next addition .
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Archaeoglobus fulgidus
UNIPROT: O28126
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The taxonomic range for the selected organisms is: Archaeoglobus fulgidus
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
hide(3 overall reactions are displayed. Show all (4)>>)
a tRNA precursor
+
CTP
=
a tRNA with a 3' cytidine end
+
diphosphate
a tRNA precursor
+
=
a tRNA with a 3' cytidine end
+
a tRNA with a 3' cytidine
+
CTP
=
a tRNA with a 3' CC end
+
diphosphate
a tRNA with a 3' cytidine
+
=
a tRNA with a 3' CC end
+
a tRNA with a 3' CC end
+
ATP
=
a tRNA with a 3' CCA end
+
diphosphate
a tRNA with a 3' CC end
+
=
a tRNA with a 3' CCA end
+
Synonyms
cca-adding enzyme, trnt1, cca enzyme, cca1p, atp(ctp):trna nucleotidyltransferase, trna-nt, class i cca-adding enzyme, ccase, afcca, ctp(atp):trna nucleotidyltransferase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ATP(CTP):tRNA nucleotidyltransferase
-
-C-C-A pyrophosphorylase
-
-
-
-
ATP(CTP)-tRNA nucleotidyltransferase
-
-
-
-
ATP:tRNA adenylyltransferase
-
-
-
-
ATP:tRNA nucleotidyltransferase (CTP)
-
-
-
-
CCA-adding enzyme
-
-
class I CCA
-
-
class I CCA enzyme
-
-
class I CCA-adding enzyme
-
-
CTP(ATP):tRNA nucleotidyltransferase
-
-
-
-
CTP:tRNA cytidylyltransferase
-
-
-
-
ribonucleic cytidylic cytidylic adenylic pyrophosphorylase
-
-
-
-
ribonucleic cytidylyltransferase
-
-
-
-
transfer ribonucleate adenyltransferase
-
-
-
-
transfer ribonucleate adenylyltransferase
-
-
-
-
transfer ribonucleate adenylyltransferase,
-
-
-
-
transfer ribonucleate cytidylyltransferase
-
-
-
-
transfer ribonucleate nucleotidyltransferase
-
-
-
-
transfer ribonucleic acid nucleotidyl transferase
-
-
-
-
transfer ribonucleic adenylyl (cytidylyl) transferase
-
-
-
-
transfer ribonucleic-terminal trinucleotide nucleotidyltransferase
-
-
-
-
transfer RNA adenylyltransferase
-
-
-
-
transfer-RNA nucleotidyltransferase
-
-
-
-
tRNA adenylyl(cytidylyl)transferase
-
-
-
-
tRNA adenylyltransferase
-
-
-
-
tRNA CCA-pyrophosphorylase
-
-
-
-
tRNA cytidylyltransferase
-
-
-
-
tRNA-nucleotidyltransferase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
a tRNA precursor + 2 CTP + ATP = a tRNA with a 3' CCA end + 3 diphosphate
show the reaction diagram
catalytic core and reaction mechanism of class I CCA-adding enzymes, overview
-
SYSTEMATIC NAME
IUBMB Comments
CTP,CTP,ATP:tRNA cytidylyl,cytidylyl,adenylyltransferase
The acylation of all tRNAs with an amino acid occurs at the terminal ribose of a 3' CCA sequence. The CCA sequence is added to the tRNA precursor by stepwise nucleotide addition performed by a single enzyme that is ubiquitous in all living organisms. Although the enzyme has the option of releasing the product after each addition, it prefers to stay bound to the product and proceed with the next addition [5].
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
a tRNA precursor + 2 CTP + ATP
a tRNA with a 3' CCA end + 3 diphosphate
show the reaction diagram
a tRNA precursor + CTP
a tRNA with a 3' cytidine end + diphosphate
show the reaction diagram
C74 addition
-
-
?
a tRNA with a 3' CC end + ATP
a tRNA with a 3' CCA end + diphosphate
show the reaction diagram
a tRNA with a 3' cytidine + CTP
a tRNA with a 3' CC end + diphosphate
show the reaction diagram
a tRNA precursor + 2 CTP + ATP
a tRNA with a 3' CCA end + 3 diphosphate
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
a tRNA precursor + 2 CTP + ATP
a tRNA with a 3' CCA end + 3 diphosphate
show the reaction diagram
-
-
-
?
additional information
?
-
-
CCA-adding enzymes recognize tRNA and tRNA-like structures as substrates, select and discriminate the correct nucleotides CTP and ATP against UTP and GTP, and, after incorporation of two C residues, the nucleotide specificity has to switch towards ATP without the help of a nucleic acid template. The enzymes have to stop polymerization exactly after three positions and recognize partial CCA-ends and add only the missing residues for completion, instead of stubbornly adding CCA-ends to their substrates, overview
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
the nature of the divalent metal ions can influence the positioning of diphosphate in the active site
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.233 - 12.5
ATP
0.01 - 0.65
CTP
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.76 - 2.72
ATP
1.83 - 3.8
CTP
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
optimal growth condition of the organismat 83°C
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
whereas CCA is added to stable tRNAs and tRNA-like transcripts, a second CCA repeat is added to certain unstable transcripts to initiate their degradation. Following the first CCA addition cycle, nucleotide binding to the active site triggers a clockwise screw motion, producing torque on the RNA. This ejects stable RNAs, whereas unstable RNAs are refolded while bound to the enzyme and subjected to a second CCA catalytic cycle. Intriguingly, with the CCA-adding enzyme acting as a molecular vise, the RNAs proofread themselves through differential responses to its interrogation between stable and unstable substrates
evolution
physiological function
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
cocrystal structures of the enzyme complexed with both a tRNA mimic and nucleoside triphosphates under catalytically active conditions. The structures suggest that adenosine 5'-monophosphate is incorporated onto the A76 position of the tRNA via a carboxylate-assisted, one-metal-ion mechanism with aspartate 110 functioning as a general base. The discrimination against incorporation of cytidine 5'-triphosphate at position 76 arises from improper placement of the a phosphate of the incoming CTP, which results from the interaction of C with arginine 224 and prevents the nucleophilic attack by the 3' hydroxyl group of cytidine75
cocrystallisation of enzyme complexes with nine distinct tRNA minihelices. All of the binary and ternary complex crystals belong to the space group P4(3)2(1)2, and contain one complex molecule in the asymmetric unit. Crystal structures are solved at 2.5 to 3.05 A resolutions by molecular replacement
crystal structures of the CCA-adding enzyme, and its complexes with CTP and ATP at 2.0, 2.0 and 2.7 A resolutions, respectively
hanging-drop vapour diffusion method at 4°C, crystal structure of the enzyme in complex with tRNA
in complex with a human MenBeta minihelix. The unstable minihelix is bound between the enzyme’s catalytic center, comprised of the head and neck domains, and its tail domain. The minihelix perfectly mimics full-length tRNA with its acceptor and TPsiC stems folding into a continuous A-type RNA helix. The TPsiC loop is in the same conformation as in full-length tRNA
crystal structure analysis
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
P295A
kcat /Km for C74 addition is 28% of wild-type value, kcat /Km for C75 addition is 33% of wild-type value, kcat /Km for A76 addition is 1% of wild-type value
P295G
kcat /Km for C74 addition is 94% of wild-type value, kcat /Km for C75 addition is 15% of wild-type value, kcat /Km for A76 addition is 129% of wild-type value
P295S
kcat /Km for C74 addition is 3% of wild-type value, kcat /Km for C75 addition is 1% of wild-type value, kcat /Km for A76 addition is 1% of wild-type value
P295T
kcat /Km for C74 addition is 36% of wild-type value, kcat /Km for C75 addition is 67% of wild-type value, kcat /Km for A76 addition is 92% of wild-type value
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant C-terminally His-tagged enzyme from Escherichia coli
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
overexpression in Escherichia coli
overexpression of C-terminally His-tagged enzyme in Escherichia coli
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Xiong, Y.; Steitz, T.A.
Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template
Nature
430
640-645
2004
Archaeoglobus fulgidus (O28126), Archaeoglobus fulgidus
Manually annotated by BRENDA team
Cho, H.D.; Chen, Y.; Varani, G.; Weiner, A.M.
A model for C74 addition by CCA-adding enzymes: C74 addition, like C75 and A76 addition, does not involve tRNA translocation
J. Biol. Chem.
281
9801-9811
2006
Archaeoglobus fulgidus
Manually annotated by BRENDA team
Pan, B.; Xiong, Y.; Steitz, T.A.
How the CCA-adding enzyme selects adenine over cytosine at position 76 of tRNA
Science
330
937-940
2010
Archaeoglobus fulgidus (O28126)
Manually annotated by BRENDA team
Mrl, M.; Betat, H.; Rammelt, C.
TRNA nucleotidyltransferases: ancient catalysts with an unusual mechanism of polymerization
Cell. Mol. Life Sci.
67
1447-1463
2010
Archaeoglobus fulgidus, Escherichia coli, Geobacillus stearothermophilus, Homo sapiens, Saccharolobus shibatae, Thermotoga maritima, Thermus thermophilus
Manually annotated by BRENDA team
Okabe, M.; Tomita, K.; Ishitani, R.; Ishii, R.; Takeuchi, N.; Arisaka, F.; Nureki, O.; Yokoyama, S.
Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure
EMBO J.
22
5918-5927
2003
Archaeoglobus fulgidus (O28126), Archaeoglobus fulgidus
Manually annotated by BRENDA team
Toh, Y.; Numata, T.; Watanabem K.; Takeshita, D.; Nureki, O.; Tomita, K.
Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme
EMBO J.
27
1944-1952
2008
Archaeoglobus fulgidus (O28126)
Manually annotated by BRENDA team
Igarashi, T.; Liu, C.; Morinaga, H.; Kim, S.; Hou, Y.
Pyrophosphorolysis of CCA addition: implication for fidelity
J. Mol. Biol.
414
28-43
2011
Archaeoglobus fulgidus, Escherichia coli, Homo sapiens
Manually annotated by BRENDA team
Cho, H.D.; Sood, V.D.; Baker, D.; Weiner, A.M.
On the role of a conserved, potentially helix-breaking residue in the tRNA-binding alpha-helix of archaeal CCA-adding enzymes
RNA
14
1284-1289
2008
Archaeoglobus fulgidus (O28126), Archaeoglobus fulgidus
Manually annotated by BRENDA team
Kuhn, C.D.; Wilusz, J.E.; Zheng, Y.; Beal, P.A.; Joshua-Tor, L.
On-enzyme refolding permits small RNA and tRNA surveillance by the CCA-adding enzyme
Cell
160
644-658
2015
Archaeoglobus fulgidus (O28126)
Manually annotated by BRENDA team