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Information on EC 6.1.1.11 - serine-tRNA ligase and Organism(s) Thermus thermophilus and UniProt Accession P34945
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6.1.1.11 serine-tRNA ligaseIUBMB Comments
This enzyme also recognizes tRNASec, the special tRNA for selenocysteine, and catalyses the formation of L-seryl-tRNASec, the substrate for EC 2.9.1.1, L-seryl-tRNASec selenium transferase.
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Word Map
- 6.1.1.11
-
raman
-
surface-enhanced
- nanoparticles
- silver
- aminoacyl-trna
- aminoacylation
-
serylation
-
colloid
- selenocysteine
-
anticodon
- trnasec
- asprs
-
isoacceptors
-
aarss
- lysyl-trna
-
roughened
- phenylalanyl-trna
- trnatyr
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langmuir-blodgett
- alanyl-trna
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handheld
- albomycins
-
citrate-reduced
- molecular biology
-
nanostars
- selenophosphate
The taxonomic range for the selected organisms is: Thermus thermophilus
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
serrs, seryl-trna synthetase, seryl trna synthetase, mtserrs, serrs2, mmbserrs, seryl-trna-synthetase, serzmo, serrs1, methanogenic serrs, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
62 kDa RNA-binding protein
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-
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Serine transfer RNA synthetase
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-
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Serine translase
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Serine--tRNA ligase
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SerRS
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SerRSmt
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SERSEC
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Seryl-transfer ribonucleate synthetase
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Seryl-transfer ribonucleic acid synthetase
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Seryl-transfer RNA synthetase
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Seryl-tRNA synthetase
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Synthetase, seryl-transfer ribonucleate
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
esterification
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Aminoacylation
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PATHWAY SOURCE
PATHWAYS
BRENDA
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-, -, -
SYSTEMATIC NAME
IUBMB Comments
L-serine:tRNASer ligase (AMP-forming)
This enzyme also recognizes tRNASec, the special tRNA for selenocysteine, and catalyses the formation of L-seryl-tRNASec, the substrate for EC 2.9.1.1, L-seryl-tRNASec selenium transferase.
CAS REGISTRY NUMBER
COMMENTARY
9023-48-7
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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
ATP + L-serine + tRNASer
AMP + diphosphate + L-seryl-tRNASer
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-
?
ATP + L-serine + tRNASer
AMP + diphosphate + L-seryl-tRNASer
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-
-
?
ATP + L-serine + tRNASer
AMP + diphosphate + L-seryl-tRNASer
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-
-
?
ATP + L-serine + tRNASer
AMP + diphosphate + L-seryl-tRNASer
a two-step reaction, seryl-tRNA synthetase is a class II synthetase depending on rather few and simple identity elements in tRNASer to determine the amino acid specificity, tRNASer acceptor stem microhelices can be aminoacylated with serine as part of the tRNA a valuable tool for investigating the structural motifs in a tRNASer-seryl-tRNA synthetase complex, tRNASer secondary structure, overview
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-
?
ATP + L-serine + tRNASer
AMP + diphosphate + L-seryl-tRNASer
formation of a seryl adenylate intermediate, mechanism of discrimination between cognate and noncognate amino acids, quantitative computational analysis, overview
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-
?
ATP + L-serine + tRNASer
AMP + diphosphate + L-seryl-tRNASer
tttRNASer
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-
?
additional information
?
-
threonine will compete with serine for formation of the activated intermediate while alanine and glycine will not compete significantly, overview, binding of ATP or seryl adenylate leads to the stabilization of a motif 2 loop that interacts with the tRNA acceptor stem
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-
?
additional information
?
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-
threonine will compete with serine for formation of the activated intermediate while alanine and glycine will not compete significantly, overview, binding of ATP or seryl adenylate leads to the stabilization of a motif 2 loop that interacts with the tRNA acceptor stem
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-
?
additional information
?
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the interaction of ttRNASer with the enzyme, interactions between the catalytically important loops and tRNA contribute to the change in dynamics of tRNA in free and bound states, respectively. These interactions help in the development of catalytically effective organization of the active site. The A76 end of the tttRNASer exhibits fast dynamics in free State, which is significantly reduced down within the active site bound with adenylate. The loops change their conformation via multimodal dynamics. Presence of bound Mg2+ ions around tRNA and dynamically slow bound water are other common features of the enzyme
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?
additional information
?
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the interaction of ttRNASer with the enzyme, interactions between the catalytically important loops and tRNA contribute to the change in dynamics of tRNA in free and bound states, respectively. These interactions help in the development of catalytically effective organization of the active site. The A76 end of the tttRNASer exhibits fast dynamics in free State, which is significantly reduced down within the active site bound with adenylate. The loops change their conformation via multimodal dynamics. Presence of bound Mg2+ ions around tRNA and dynamically slow bound water are other common features of the enzyme
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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
ATP + L-serine + tRNASer
AMP + diphosphate + L-seryl-tRNASer
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-
-
?
ATP + L-serine + tRNASer
AMP + diphosphate + L-seryl-tRNASer
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-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ATP
binding of ATP leads to the stabilization of a motif 2 loop that interacts with the tRNA acceptor stem
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mn2+
-
the enzyme complexes: 1. with ATP and Mn2+, 2. containing seryl-adenylate in the active site, 3. between the enzyme, Ap4A and Mn2+, exhibit a common Mn2+-site in which the cation is coordinated by two active-site residues in addition to the alpha-phosphate group from the bound ligands
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
calculated binding energies in the activated mode agrees with kinetic measurements of a covalent bond between the amino acid and ATP, quantitative computational analysis of amino acid binding, overview
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additional information
additional information
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calculated binding energies in the activated mode agrees with kinetic measurements of a covalent bond between the amino acid and ATP, quantitative computational analysis of amino acid binding, overview
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
the enzyme belongs to the class II, subclass IIa, of aminoacyl-tRNA sythetases
additional information
additional information
the interactions between the catalytically important loops and tRNA contribute to the change in dynamics of tRNA in free and bound states, respectively. These interactions help in the development of catalytically effective organization of the active site. The A76 end of the tttRNASer exhibits fast dynamics in free state, which is significantly reduced within the active site bound with adenylate. Presence of bound Mg2+ ions around tRNA and dynamically slow bound water are other common features of the enzyme, dynamics of dimeric ttSerRS bound with adenylate and tttRNASer with a focus to the molecular process of the dynamic development of the catalytically competent active site organization essential for the second step, molecular dynamic simulations, overview
additional information
-
the interactions between the catalytically important loops and tRNA contribute to the change in dynamics of tRNA in free and bound states, respectively. These interactions help in the development of catalytically effective organization of the active site. The A76 end of the tttRNASer exhibits fast dynamics in free state, which is significantly reduced within the active site bound with adenylate. Presence of bound Mg2+ ions around tRNA and dynamically slow bound water are other common features of the enzyme, dynamics of dimeric ttSerRS bound with adenylate and tttRNASer with a focus to the molecular process of the dynamic development of the catalytically competent active site organization essential for the second step, molecular dynamic simulations, overview
PDB
SCOP
CATH
UNIPROT
ORGANISM
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure analysis for identification of the amino acid substrate discrimination mechanism
tRNASer-seryl-tRNA synthetase complex, X-ray diffraction structure determination and analysis at 2.9 A resolution, the 1.8 A-resolution tRNASer acceptor stem crystal structure is superimposed to a 2.9 A-resolution crystal structure of a tRNASer-seryl-tRNA synthetase complex for a visualization of the binding environment of the tRNASer microhelix, modeling
enzyme complexes: 1. with seryl-AMP, 2. with 5'-O-[N-(L-seryl)-sulfamoyl]adenosine
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structure at 2.3-2.6 A resolution, of enzyme complexes: 1. with ATP and Mn2+, 2. containing seryl-adenylate in the active site, 3. between the enzyme, Ap4A and Mn2+
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Belrhali, H.; Yaremchuk, A.; Tukalo, M.; Berthet-Colominas, C.; Rasmussen, B.; Bsecke, P.; Diat, O.; Cusack, S.
The structural basis for seryl-adenylate and Ap4A synthesis by seryl-tRNA synthetase
Structure
3
341-352
1995
Escherichia coli, Thermus thermophilus
Lenhard, B.; Filipic, S.; Landeka, I.; Skrtic, I.; Sll, D.; Weygand-Durasevic, I.
Defining the active site of yeast seryl-tRNA synthetase. Mutations in motif 2 loop residues affect tRNA-dependent amino acid recognition
J. Biol. Chem.
272
1136-1141
1997
Saccharomyces cerevisiae, Thermus thermophilus (P34945), Thermus thermophilus
Belrhali, H.; Yaremchuk, A.; Tukalo, M.; Larsen, K.; Berthet-Colominas, C.; Leberman, R.; Beijer, B.; Sproat, B.; Als-Nielsen, J.; Grubel, G.; Legrand, J.F.; Lehman, M.; Cusack, S.
Crystal structures at 2.5 Angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate
Science
263
1432-1436
1994
Thermus thermophilus
Foerster, C.; Brauer, A.B.; Fuerste, J.P.; Betzel, C.h.; Weber, M.; Cordes, F.; Erdmann, V.A.
Superposition of a tRNASer acceptor stem microhelix into the seryl-tRNA synthetase complex
Biochem. Biophys. Res. Commun.
362
415-418
2007
Thermus thermophilus (P34945)
McClendon, C.L.; Vaidehi, N.; Kam, V.W.; Zhang, D.; Goddard, W.A.
Fidelity of seryl-tRNA synthetase to binding of natural amino acids from HierDock first principles computations
Protein Eng. Des. Sel.
19
195-203
2006
Saccharomyces cerevisiae, Thermus thermophilus (P34945), Thermus thermophilus
Dutta, S.; Nandi, N.
Classical molecular dynamics simulation of seryl tRNA synthetase and threonyl tRNA synthetase bound with tRNA and aminoacyl adenylate
J. Biomol. Struct. Dyn.
2018
1-23
2018
Thermus thermophilus (P34945), Thermus thermophilus, Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 (P34945), Thermus thermophilus DSM 7039 (P34945)
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