Flexible 3D structure of Bos taurus tyrosyl-tRNA synthetase suggests the existence of the hinge mechanism provided by conservative Gly353 at interdomain linker
Mammalian tyrosyl-tRNA synthetase is composed of two structural modules: N-terminal catalytic miniTyrRS and non-catalytic cytokine-like C-terminal module connected by a flexible peptide linker. Till now, the 3D structure of any full-length mammalian TyrRS has not been solved by X-ray crystallography...
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irk-123456789-1569422019-06-20T01:27:19Z Flexible 3D structure of Bos taurus tyrosyl-tRNA synthetase suggests the existence of the hinge mechanism provided by conservative Gly353 at interdomain linker Pydiura, N.A. Kornelyuk, A.I. Bioinformatics Mammalian tyrosyl-tRNA synthetase is composed of two structural modules: N-terminal catalytic miniTyrRS and non-catalytic cytokine-like C-terminal module connected by a flexible peptide linker. Till now, the 3D structure of any full-length mammalian TyrRS has not been solved by X-ray crystallography. The aim of this work was a homology modeling of 3D structure of full-lehgth B. taurus tyrosyl-tRNA synthetase. Methods. Homology modeling of TyrRS was performed by Modeller 9.1 package. Quality of the models was assessed using Biotech Validation Suite web-server. Results. Our BLAST search identified 34 % sequence homology between interdomain linker of TyrRS and linker of human c-Abl tyrosine kinase. In order to model the full-length TyrRS structure we assembled the models of three parts of the protein (N- and C- terminal domains and the linker) using Modeller 9.1 software. The best Abl-17 model structure was refined by energy minimization. Conclusions. High flexibility of the interdomain linker can generate multiple conformations of TyrRS. The hinge mechanism at interdomain linker may be provided by conservative Gly353. It is proposed, that due to the linker flexibility an open extended conformation of TyrRS could transform into closed conformations in the enzyme-substrate complexes. Тирозил-тРНК синтетаза (TyrRS) ссавців складається з двох структурних модулів: N-кінцевого каталітичного модуля (mini TyrRS) і некаталітичного цитокін-подібного C-кінцевого модуля, з’єднаних гнучким пептидним лінкером. До сьогодні просторову структуру повнорозмірної TyrRS ссавців не вирішено методом рентгенівської кристалографії. Мета цієї роботи полягала в моделюванні за гомологією просторової структури повнорозмірної TyrRS B. taurus. Методи. Моделювання за гомологією TyrRS проведено з використанням Modeller 9.1. Якість моделей оцінювали за допомогою Biotech Validation Suite web-сервера. Результати. За даними BLAST-пошуку визначено 34 %-ву гомологію послідовності міждоменного лінкера TyrRS і лінкера c-Abl тирозинкінази людини. Для моделювання структури повнорозмірної TyrRS ми зібрали модель з трьох фрагментів білка (N-і С-кінцевих доменів і міждоменного лінкера), використовуючи Modeller 9.1. Кращу модель структури Abl-17 уточнено методом мінімізації енергії. Висновки. Висока гнучкість міждоменного лінкера може призводити до формування множинних конформацій TyrRS. Шарнірний механізм у міждоменному лінкері, вірогідно, забезпечується консервативним залишком Gly353. Передбачається, що завдяки високій гнучкості міждоменного лінкера відкрита конформація TyrRS може переходити в закриту конформацію у ферментно-субстратних комплексах. Тирозил-тРНК синтетаза (TyrRS) млекопитающих состоит из двух структурных модулей: N-концевого каталитического модуля (miniTyrRS) и некаталитического цитокин-подобного C-концевого модуля, соединенных гибким пептидным линкером. До настоящего времени пространственная структура полноразмерной TyrRS млекопитающих не решена методом рентгеновской кристаллографии. Цель данной работы состояла в моделировании по гомологии пространственной структуры полноразмерной TyrRS B. taurus. Методы. Моделирование по гомологии TyrRS выполнено с помощью пакета Modeller 9.1. Качество моделей оценивали с помощью Biotech Validation Suite web-сервера. Результаты. По данным BLAST-поиска определена 34 %-я гомология последовательности междоменного линкера TyrRS и линкера c-Abl тирозинкиназы человека. Для моделирования структуры полноразмерной TyrRS, мы собрали модель из трех фрагментов белка (N- и С-концевых доменов и междоменного линкера), используя Modeller 9.1. Лучшая модель структуры Abl-17 уточнена методом минимизации энергии. Выводы. Высокая гибкость междоменного линкера может приводить к формированию множественных конформаций TyrRS. Шарнирный механизм в междоменном линкере, вероятно, обеспечивается консервативным остатком Gly 353. Предполагается, что из-за высокой гибкости междоменного линкера открытая конформация TyrRS может переходить в закрытую конформацию в ферментно-субстратных комплексах. 2012 Article Flexible 3D structure of Bos taurus tyrosyl-tRNA synthetase suggests the existence of the hinge mechanism provided by conservative Gly353 at interdomain linker / N.A. Pydiura, A.I. Kornelyuk // Вiopolymers and Cell. — 2012. — Т. 28, № 5. — С. 397-403. — Бібліогр.: 35 назв. — англ. 0233-7657 DOI: http://dx.doi.org/10.7124/bc.000076 http://dspace.nbuv.gov.ua/handle/123456789/156942 577.152:611.576.31 en Вiopolymers and Cell Інститут молекулярної біології і генетики НАН України |
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Bioinformatics Bioinformatics Pydiura, N.A. Kornelyuk, A.I. Flexible 3D structure of Bos taurus tyrosyl-tRNA synthetase suggests the existence of the hinge mechanism provided by conservative Gly353 at interdomain linker Вiopolymers and Cell |
| description |
Mammalian tyrosyl-tRNA synthetase is composed of two structural modules: N-terminal catalytic miniTyrRS and non-catalytic cytokine-like C-terminal module connected by a flexible peptide linker. Till now, the 3D structure of any full-length mammalian TyrRS has not been solved by X-ray crystallography. The aim of this work was a homology modeling of 3D structure of full-lehgth B. taurus tyrosyl-tRNA synthetase. Methods. Homology modeling of TyrRS was performed by Modeller 9.1 package. Quality of the models was assessed using Biotech Validation Suite web-server. Results. Our BLAST search identified 34 % sequence homology between interdomain linker of TyrRS and linker of human c-Abl tyrosine kinase. In order to model the full-length TyrRS structure we assembled the models of three parts of the protein (N- and C- terminal domains and the linker) using Modeller 9.1 software. The best Abl-17 model structure was refined by energy minimization. Conclusions. High flexibility of the interdomain linker can generate multiple conformations of TyrRS. The hinge mechanism at interdomain linker may be provided by conservative Gly353. It is proposed, that due to the linker flexibility an open extended conformation of TyrRS could transform into closed conformations in the enzyme-substrate complexes. |
| format |
Article |
| author |
Pydiura, N.A. Kornelyuk, A.I. |
| author_facet |
Pydiura, N.A. Kornelyuk, A.I. |
| author_sort |
Pydiura, N.A. |
| title |
Flexible 3D structure of Bos taurus tyrosyl-tRNA synthetase suggests the existence of the hinge mechanism provided by conservative Gly353 at interdomain linker |
| title_short |
Flexible 3D structure of Bos taurus tyrosyl-tRNA synthetase suggests the existence of the hinge mechanism provided by conservative Gly353 at interdomain linker |
| title_full |
Flexible 3D structure of Bos taurus tyrosyl-tRNA synthetase suggests the existence of the hinge mechanism provided by conservative Gly353 at interdomain linker |
| title_fullStr |
Flexible 3D structure of Bos taurus tyrosyl-tRNA synthetase suggests the existence of the hinge mechanism provided by conservative Gly353 at interdomain linker |
| title_full_unstemmed |
Flexible 3D structure of Bos taurus tyrosyl-tRNA synthetase suggests the existence of the hinge mechanism provided by conservative Gly353 at interdomain linker |
| title_sort |
flexible 3d structure of bos taurus tyrosyl-trna synthetase suggests the existence of the hinge mechanism provided by conservative gly353 at interdomain linker |
| publisher |
Інститут молекулярної біології і генетики НАН України |
| publishDate |
2012 |
| topic_facet |
Bioinformatics |
| url |
http://dspace.nbuv.gov.ua/handle/123456789/156942 |
| citation_txt |
Flexible 3D structure of Bos taurus tyrosyl-tRNA
synthetase suggests the existence of the hinge mechanism
provided by conservative Gly353 at interdomain linker / N.A. Pydiura, A.I. Kornelyuk // Вiopolymers and Cell. — 2012. — Т. 28, № 5. — С. 397-403. — Бібліогр.: 35 назв. — англ. |
| series |
Вiopolymers and Cell |
| work_keys_str_mv |
AT pydiurana flexible3dstructureofbostaurustyrosyltrnasynthetasesuggeststheexistenceofthehingemechanismprovidedbyconservativegly353atinterdomainlinker AT kornelyukai flexible3dstructureofbostaurustyrosyltrnasynthetasesuggeststheexistenceofthehingemechanismprovidedbyconservativegly353atinterdomainlinker |
| first_indexed |
2025-07-14T09:18:28Z |
| last_indexed |
2025-07-14T09:18:28Z |
| _version_ |
1837613407143985152 |
| fulltext |
397
BIOINFORMATICS
UDC 577.152:611.576.31
Flexible 3D structure of Bos taurus tyrosyl-tRNA
synthetase suggests the existence of the hinge mechanism
provided by conservative Gly353 at interdomain linker
N. A. Pydiura, A. I. Kornelyuk
Institute of Molecular Biology and Genetics, NAS of Ukraine
150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
kornelyuk@imbg.org.ua
Mammalian tyrosyl-tRNA synthetase is composed of two structural modules: N-terminal catalytic miniTyrRS and
non-catalytic cytokine-like C-terminal module connected by a flexible peptide linker. Till now, the 3D structure
of any full-length mammalian TyrRS has not been solved by X-ray crystallography. The aim of this work was a ho-
mology modeling of 3D structure of full-lehgth B.taurus tyrosyl-tRNA synthetase. Methods. Homology modeling
of TyrRS was performed by Modeller 9.1 package. Quality of the models was assessed using Biotech Validation
Suite web-server. Results. Our BLAST search identified 34% sequence homology between interdomain linker of
TyrRS and linker of human c-Abl tyrosine kinase. In order to model the full-length TyrRS structure we as-
sembled the models of three parts of the protein (N- and C- terminal domains and the linker) using Modeller 9.1
software. The best Abl-17 model structure was refined by energy minimization. Conclusions. High flexibility of
the interdomain linker can generate multiple conformations of TyrRS. The hinge mechanism at interdomain
linker may be provided by conservative Gly353. It is proposed, that due to the linker flexibility an open extended
conformation of TyrRS could transform into closed conformations in the enzyme-substrate complexes.
Keywords: tyrosyl-tRNA synthetase, homology modeling, interdomain linker, c-Abl tyrosine kinase, EMAP II,
tRNA
Tyr
.
Introduction. Tyrosyl-tRNA synthetase (TyrRS, EC
6.1.1.1) is one of the key enzymes of protein biosyn-
thesis in both pro- and eukaryotes [1]. Bovine (B. tau-
rus) cytoplasmic TyrRS is one of the best studied mam-
malian aminoacyl-tRNA synthetases. This enzyme
forms a homodimer of two 59.2 kDa subunits, each of
528 amino acid (aa) residues. N- and C-terminal do-
mains of the enzyme subunit are connected by a long
disordered 17 aa linker (Fig. 1, a) [1]. The NH2-termi-
nal catalytic domain comprises a «minimal» 39 kDa
TyrRS and has full catalytic activity in vitro [1, 2]. The
C-terminal domain formed by aa residues Val363-
Ser528 is 166 aa long [3] and reveals the 52.7 % iden-
tity to the mammalian cytokine endothelial monocyte-
activating polypeptide II (EMAPII) [4, 5], which activa-
tes monocytes and endothelial cells – an effect first dis-
covered at cancerogenesis induced with chemicals [6, 7].
A multiple alignment of C-domains guided by pre-
dicted secondary structure revealed two independent sub-
domains (folds): a �-pleated Myf domain (OB-fold, re-
sidues Val363-Lys470) and �-helical sub-domain (re-
sidues Gly471-Ser528) [3]. Myf domain and �-helical
sub-domain form the RNA binding surface. A lysine-
rich cluster KPKKK located within the sub-domain may
play a role of a nuclear localization signal [8]. Several
organisms posess C-terminal domain homologous to
that of TyrRS. There are experimental data showing
involvement of Arc1p (G4p1) from Saccharomyces ce-
revisiae (55.3 % identity) [10], human p43 (pro-
EMAPII) (62.7 %) [3], and ARCE from Euplotes
octocarinatus (52 %) [11] in non-specific tRNA bin-
ding. These proteins direct tRNA to the active sites of
corresponding aminoacyl-tRNA synthetases [10, 12].
It is possible, that during the evolution C-terminal do-
main was transferred to several diverse proteins invol-
ved in translation (such as TyrRS, MetRS, p43, and
ISSN 0233–7657. Biopolymers and Cell. 2012. Vol. 28. N 5. P. 397–403
� Institute of Molecular Biology and Genetics, NAS of Ukraine, 2012
398
PYDIURA N. A., KORNELYUK A. I.
Arc1p) to enable their proper functioning in higher eu-
karyotes [3]. Bovine C-domain contributes about 50 %
of TyrRS affinity to ribosomal RNAs. RNA binding has
a certain specificity: among others, poly(G) has the most
inhibitory effect in the reaction of tRNATyr amino-
acylation [13].
At present there are more than 40 three-dimensional
structures of diverse aminoacyl-tRNA synthetases depo-
sited in PDB. Unfortunately, no structure of full-length
mammalian TyrRS has been solved by experimental
means. The difficulties of obtaining crystals can be cau-
sed by the presence of transiently disordered labile 17-
aa long linker between N- and C-terminal domains. A
large size of the protein makes NMR approach to the
structure determination difficult, if not altogether im-
practical. Mobility and flexibility of this linker may be
required for the adaptable orientation of domains neces-
sary for aminoacylation reaction. It is noteworthy that
the linker is accessible to specific proteinases and con-
tains a putative proteolytic PEST sequence [8]. Despite
all the experimental information gathered up to date,
there is no clear understanding either C-domain or inter-
domain linker role and mode of action. The significan-
ce of linker relation to both cytokine motives and tRNA-
binding domains is unclear and needs to be explained.
The absence of experimentally derived full-length struc-
ture and importance of understanding a role of these
two eukaryotic cytokine motives justify computational
approach to the study of mammalian cytoplasmic TyrRS.
An accurate model will allow further investigation of
TyrRS properties, suggest biochemical, biophysical and
computational experiments and may lead to elucidation
of its mechanism of action.
Materials and methods. The amino acid sequence
of bovine TyrRS was reported earlier [3, 9] (Entrez
(http://www.ncbi.nlm.nih.gov/entrez/), accession num-
ber Q29465). The sequence has been analyzed for pos-
sible intrinsically disordered regions by DISPROT
predictor VSL2B (http://www.ist.temple.edu/disprot/
predictorVSL2.php) [14] and IUPPRED (http://iupred.
enzim.hu/) [15] web-servers.
We used Internet web-servers such as BLAST (http:
//www.ncbi.nim.nih.gov/BLAST) and PDB-BLAST
(http://www.ebi.ac.uk/pdb) to search for homologous
sequences. Three-dimensional coordinates of the pro-
tein structural templates were downloaded from Protein
Rossman fold �-helical domain OB-fold domain A-subdomain 528 a.a.
N-terminal module Linker C-terminal module
a
b
c
d
Fig. 1. a – Schematic representation of a single subunit domain organization of Bos taurus cytoplasmic TyrRS (Rossmann fold of the N-terminal
domain is followed by the anticodon binding �-helical fold; the interdomain linker of 17 aa links N-module to the C-terminal domain comprised
of the OB-fold and A-subdomain); b – pairwise sequence alignment of the bovine TyrRS N-terminal domain with the corresponding human
sequence (PDB code 1N3L); c – sequence alignment between the catalytic loop sequence of N-terminal domain of TyrRS and the un-
characterized protein from Bacillus cereus loop (PDB code 1X7F); d – the alignment of the sequences of bovine TyrRS C-terminal domain with
the corresponding human sequence (PDB code 1NTG_A). The alignment was made by ClustalW2 program [23, 24], the secondary structure
information was obtained from PDB
399
FLEXIBLE 3D STRUCTURE OF Bos taurus TYROSYL-tRNA SYNTHETASE
Data Bank (PDB) (http://www.pdb.org/pdb) [16]. A
rigid alignment of TyrRSs 3D structures was carried out
using function «Fit/Iterative Magic Fit/C� atoms only»
of Swiss-PdbViewer 4.0.1 (http://expasy.org/spdbv/)
[17]. Images were prepared with PyMOL software [18]
and POV-Ray [19]. Electrostatic potentials were cal-
culated using APBS [20, 21].
To build 3D models of full-length bovine TyrRS
we used homology modeling techniques [22]. Multiple
alignments were done using ClustalW server (http://
www2.ebi.ac.uk/clustalw/) [23, 24]. A search for homo-
logues was performed using above described tools and
the resulting templates were used to model TyrRS by
Modeller 9.1 package [25]. Quality of the models was as-
sessed using Biotech Validation Suite web-server (http:
//biotech.ebi.ac.uk). Ramachandran plots were built using
PROCHECK [26].
Our approach to full-length TyrRS modeling can be
outlined as follows: separate prediction of N- and C-do-
mains 3D structures based on experimentally solved
highly homologous structures, prediction of interdo-
main linker followed by the assembly of full-length pro-
tein models.
Both domains of bovine TyrRS are well studied and
their sequences bear high degree of homology to corres-
ponding human TyrRS domains. We used two crystallo-
graphic structures deposited in PDB (codes 1N3L and
1NTG, chain A) as templates for homology modeling
of the bovine N- and C-terminal domains correspon-
dingly [27, 28]. These pairs of sequences are highly ho-
mologues and their modeling causes no significant pro-
blem. An alignment of bovine N-terminal domain to hu-
man 1N3L is shown on Fig. 1, b. The homology between
the two domains is 95 %.
A crystal structure of the human N-terminal domain
reported as 1N3L lacks 7 aa of the catalytic loop. We op-
ted not to close this loop de novo, but instead searched
for homologues in the PDB. The PDB was queried by a
catalytic loop sequence plus 5-aa overhangs at each
side: GLTGSKMSSSEEESKID. The search resulted in
about 100 sequences with 70 unique ones. The sequen-
ces with low homology to catalytic loop itself were dis-
carded. The best homologues were selected for further
analysis (PDB codes 2BBO (chain A, human Nbd1 with
Phe508), 2DBG (chain A, pyrin Paad-Dapin domain),
1PS9 (chain A), 1POY (chain 1, spermidine-putresci-
ne-binding protein), 1X7F (chain A, an uncharacteri-
zed Bacillus cereus protein)). Two structures, 1X7F
and 1POY, containing turns in their loops, were consi-
dered. The 41 % homologous 1X7F [29] was selected
for actual modeling due to gapless alignment with bo-
vine TyrRS linker (Fig. 1, c). For the N-domain we
generated 10 models and selected a model number 8 as
having the optimal Modeller objective function score
and the best Biotech Validation Suite score (objective =
= 1490, Biotech = 1.38).
The C-terminal domain was aligned with cytokine-
like human 1NTG_A (Fig. 2, a) with 92 % identity. Ten
slightly different models of each domain were obtai-
ned. Selection of the models for future use was based
on Biotech scores and Modeller objective function. A
model number 5 was selected (objective = 934, Bio-
tech = 1.28).
Modeling the interdomain linker of 17 aa was much
more problematic. To model its structure we used two
different approaches. A straightforward template-based
approach commenced with BLAST search of all known
linkers and identified a fragment of an auto-inhibitor of
human C-Abl tyrosine kinase as the best template (PDB
code 1OPL, chain A) [30]. To enable the modeling we
added 5-aa overlaps to each side of the linker sequence.
Resulting homology between the two sequences was
Thr231
Ala236
Asp252
Met256
a b
Fig. 2. a – Alignment of the sequences of bovine TyrRS interdomain linker with the linker derived from auto-inhibitor of human C-Abl tyrosine
kinase (PDB code 1OPL_A); b – 3D structure of the human C-Abl kinase linker, residues Ile229-Met256 (PDB code 1OPL_A). The structure
corresponding to the TyrRS linker is shown in magenta
only 34 % (Fig. 1, d). The first model was selected from
the ten models obtained, with objective = 3700, Bio-
tech = 1.20. The C-Abl kinase linker structure is shown
in Fig. 2, b.
In order to model the full-length TyrRS protein we
assembled all three parts (C-, and N-domains and lin-
ker) using Modeller 9.1. To get a realistic domain
orientation we strived to obtain a maximum overlaps of
the linker terminal amino acids backbone � and �
torsion angles with corresponding amino acids of do-
mains being attached. All models were refined by ener-
gy minimization in Swiss-PDB Viewer [17] until their
potential energy converged to an average value of ap-
proximately –23700 kJ/mol.
Results and discussion. The failed efforts to crys-
tallize full-length bovine TyrRS, as well as preliminary
NMR data obtained in our laboratory (unpublished)
made us suspect that the protein has intrinsically or tran-
siently disordered regions. We have carried out bioin-
formatics analysis of potential TyrRS disorder. The da-
ta are analogous to those obtained for human TyrRS
[31] and are shown in Fig. 3. The main unfolded regions
correspond to the N- and C-termini, catalytic loop (Pro
216-Glu229) and interdomain linker (Pro342-Glu362) of
the protein. The linker flexibility may be necessary for
correct mutual orientation of N- and C- domains during
tRNATyr binding and recognition. We decided to build
an ensemble of possible linker conformations based on
the homology with human C-Abl kinase linker (homo-
logy models will be further designated as Abl-X).
All homology models of full-length bovine TyrRS
were generated in Modeller 9.1 from four components:
N-terminal domain, catalytic loop, linker structure and
the C-domain as described in Materials and methods. A
selected model was refined by minimization in Swiss-
PDB Viewer 4.0.1 (GROMOS96 43B1 parameter set)
until its free energy reached a plateau. An average final
energy for selected Abl-17 model was –23700 kJ/mol.
This model is characterized as extended («open») structu-
re. It is possible that the solvated linker makes positive con-
tribution to the overall structure free energy. The mutual
orientation of two domains in Abl-17 is shown in Fig. 4.
Earlier, some putative tRNATyr binding residues of
the C-domain were predicted from the tRNAPhe and
tRNATyr modification protection experiments [32].
Structural analysis of the tRNA-C-domain complex re-
vealed a potential tRNA binding surface which consists
of �'1-�'2 hairpin (Leu426-Gly433, Lys435-Gln437)
400
PYDIURA N. A., KORNELYUK A. I.
Residue position
D
is
o
rd
e
r
te
n
d
en
cy
0 100 200 300 400 500
1
0
0.2
0.4
0.6
0.8
1
0
0.2
0.4
0.6
0.8
D
is
o
rd
e
r
p
ro
b
a
b
il
it
y
Residue position
0 100 200 300 400 500
DISPROT – disorder prediction resultsa b
Fig. 3. Results of the bovine TyrRS protein intrinsically disordered region prediction by IUPRED [14] (a) and by VSL2B program of DISPROT
server [15] (b). The values above a middle line correspond to the intrinsically disordered regions of the protein
C-module
N-module
Reconstructed
catalytic loop
Gly353
Interdomain
linker
Fig. 4. Refined model Abl-17 of the full-length TyrRS colored accor-
ding to secondary structure (�-helices,�-strands and turns are red, blue
and grey respectively). The reconstructed catalytic loop is shown as
blue sticks. The conservative glycine-353 in the interdomain linker is
shown as green vdW-spheres
inserted into OB fold, interdomain region (Glu480-
Leu481), KPKKK lysine-rich cluster and Glu489-
Lys490 residues of the �-helix of A-sub-domain. N-
Domain is responsible for the specific recognition and
binding of L-tyrosine (residues Tyr39, Tyr166, Gln170,
Asp173, and Gln188). The contact surface of the N-mo-
dule with tRNATyr is formed by 14 aa, which are homo-
logous to the corresponding residues in the yeast TyrRS
(His158, Lys246-Pro252, Trp283, His305-Asp308, and
Lys310) (Fig. 5, a). An evolutionary conservative
Trp283 residue should form a stacking interaction with
G34 of the tRNA, while a conservative Asp308 – hydro-
gen bonds with the same nucleotide.
We have superimposed the selected models on the
crystallographic structure of the human TyrRS N-do-
main dimer 1N3L with the N-domain structure as a re-
ference. Conformations of the side chains of initial mo-
del, which made clashes on the interface of N-modules
in the dimer were optimized by Swiss-PdbViewer «si-
mulated annealing» procedure. It was found that the
Abl-17 structure had C-domain in the proximity with
RNA binding surface of N-domain. The «open» structu-
re of Abl-17 can form a large positively charged conti-
nuous RNA binding surface (Fig. 5, b).
Since the flexibility of the linker is able to rotate
around pivotal glycine-353 we do not consider the mu-
tual domain orientation to be fixed. We have analyzed
TyrRS interdomain linker sequences from 22 species
of Metazoa (Fig. 6). In all Chordata the glycine posi-
tion at the linker is absolutely conserved, which points
out to its functional importance. Other Metazoa linkers
also contain glycine, several amino acids shifted up- or
downwards from the homologues of the Gly353. The
shorter linker length in insects probably reflects a more
ancient variant, while acquired prolines and lysines and
linker extension in chordates result in more flexible
linker backbone, probably needed for more adaptable in-
teraction with different structural elements of tRNATyr.
It is possible that flexibility of the linker plays an
important role in the interdomain communications and
dynamic coupling/uncoupling between the N- and C-
domains, analogously to the effect observed in Csk ki-
nase [33]. Class Ic of aminoacyl-tRNA synthetases re-
cognizes the tRNA anticodon by one subunit and this
«signal» has to be somehow transferred to the other
subunit. There should be a mechanism of adaptable dy-
namic juxtaposition of the two subunits and the struc-
tural analysis of the interdomain linker gives us a hint
at possible mechanism. The presence of four exposed
lysine moieties in the linker of «open» conformation
allows us to hypothesize a non-specific tRNA binding
by the linker. On the other hand, the interdomain linker
contains a proPEST motive and can be cleaved by pro-
teases to release a cytokine-like C-domain. The flexibi-
lity of the linker may modulate accessibility and expo-
sure of this proteolysis site.
The full-length model of bovine TyrRS, as well as
both its domains separately, can be used for further ana-
lysis and computational experiments, such as molecu-
lar docking with tRNATyr, molecular dynamics simu-
lations etc. Recently, we have performed an analysis of
the YCD2 fragment of this model, comprised of the
�-helical part of N-domain, the linker and the C-do-
main. The results reported in [34], revealed a specific
behavior of the linker in ten-nanosecond time-frame. It
changes conformation from extended and disordered to
more compact one with short transient �-helical struc-
tures, supporting the currently proposed general model
401
FLEXIBLE 3D STRUCTURE OF Bos taurus TYROSYL-tRNA SYNTHETASE
a b
Fig. 5. a – The molecular surface of Tyr RS
Abl-17 model structure (the parts of N-
and C-modules which probably form the
tRNA binding surface (His158, Lys
246-Pro252, Trp283, His305-Asp308, Lys
310, Leu426-Gly433, Lys435-Gln437,
Glu480-Lys486, and Glu489-Lys490) are
shown in green; positively charged resi-
dues are blue, negative – red); b – the mo-
lecular surface of TyrRS dimer obtained
by superimposition of Abl-17 model onto
crystallographic model 1N3L (colour
figure at www.biopolymers.org.ua)
of the interdomain linker role in modulation of the enzy-
me activity [35].
Future study on the full-length model of TyrRS mo-
lecules by molecular dynamics, with obtained structu-
res as starting points, will hopefully allow us to suggest
a mechanism of tyrosyl-tRNA synthetase action.
Acknowledgements. This work was supported by
the National Academy of Sciences of Ukraine within
the project «Dynamic aspects of functioning of
eukaryotic tyrosyl-tRNA synthetase» (registration
number 0107 U004938).
Ì. Î. Ïèäþðà, Î. ². Êîðíåëþê
Ãíó÷êà ïðîñòîðîâà ñòðóêòóðà Bos taurus òèðîçèë-òÐÍÊ ñèíòåòàçè
ïðèïóñêຠ³ñíóâàííÿ øàðí³ðíîãî ìåõàí³çìó, ÿêèé
çàáåçïå÷óºòüñÿ êîíñåðâàòèâíèì Gly353 ó ì³æäîìåííîìó ë³íêåð³
Ðåçþìå
Òèðîçèë-òÐÍÊ ñèíòåòàçà (TyrRS) ññàâö³â ñêëàäàºòüñÿ ç äâîõ
ñòðóêòóðíèõ ìîäóë³â: N-ê³íöåâîãî êàòàë³òè÷íîãî ìîäóëÿ (mini
TyrRS) ³ íåêàòàë³òè÷íîãî öèòîê³í-ïîä³áíîãî C-ê³íöåâîãî ìîäóëÿ,
ç’ºäíàíèõ ãíó÷êèì ïåïòèäíèì ë³íêåðîì. Äî ñüîãîäí³ ïðîñòîðîâó
ñòðóêòóðó ïîâíîðîçì³ðíî¿ TyrRS ññàâö³â íå âèð³øåíî ìåòîäîì
ðåíòãåí³âñüêî¿ êðèñòàëîãðàô³¿. Ìåòà ö³º¿ ðîáîòè ïîëÿãàëà â ìî-
äåëþâàíí³ çà ãîìîëî㳺þ ïðîñòîðîâî¿ ñòðóêòóðè ïîâíîðîçì³ðíî¿
TyrRS B. taurus. Ìåòîäè. Ìîäåëþâàííÿ çà ãîìîëî㳺þ TyrRS ïðî-
âåäåíî ç âèêîðèñòàííÿì Modeller 9.1. ßê³ñòü ìîäåëåé îö³íþâàëè
çà äîïîìîãîþ Biotech Validation Suite web-ñåðâåðà. Ðåçóëüòàòè.
Çà äàíèìè BLAST-ïîøóêó âèçíà÷åíî 34 %-âó ãîìîëîã³þ ïîñë³äîâ-
íîñò³ ì³æäîìåííîãî ë³íêåðà TyrRS ³ ë³íêåðà c-Abl òèðîçèíê³íàçè
ëþäèíè. Äëÿ ìîäåëþâàííÿ ñòðóêòóðè ïîâíîðîçì³ðíî¿ TyrRS ìè
ç³áðàëè ìîäåëü ç òðüîõ ôðàãìåíò³â á³ëêà (N-³ Ñ-ê³íöåâèõ äîìåí³â ³
ì³æäîìåííîãî ë³íêåðà), âèêîðèñòîâóþ÷è Modeller 9.1. Êðàùó ìî-
äåëü ñòðóêòóðè Abl-17 óòî÷íåíî ìåòîäîì ì³í³ì³çàö³¿ åíåð㳿.
Âèñíîâêè. Âèñîêà ãíó÷ê³ñòü ì³æäîìåííîãî ë³íêåðà ìîæå ïðèçâî-
äèòè äî ôîðìóâàííÿ ìíîæèííèõ êîíôîðìàö³é TyrRS. Øàðí³ðíèé
ìåõàí³çì ó ì³æäîìåííîìó ë³íêåð³, â³ðîã³äíî, çàáåçïå÷óºòüñÿ êîí-
ñåðâàòèâíèì çàëèøêîì Gly353. Ïåðåäáà÷àºòüñÿ, ùî çàâäÿêè âè-
ñîê³é ãíó÷êîñò³ ì³æäîìåííîãî ë³íêåðà â³äêðèòà êîíôîðìàö³ÿ
TyrRS ìîæå ïåðåõîäèòè â çàêðèòó êîíôîðìàö³þ ó ôåðìåíòíî-
ñóáñòðàòíèõ êîìïëåêñàõ.
Êëþ÷îâ³ ñëîâà: òèðîçèë-òÐÍÊ ñèíòåòàçà, ìîäåëþâàííÿ çà
ãîìîëî㳺þ, ì³æäîìåííèé ë³íêåð, c-Abl òèðîçèíê³íàçà, EMAP II,
òÐÍÊ
Tyr
.
Í. À. Ïèäþðà, À. È. Êîðíåëþê
Ãèáêàÿ ïðîñòðàíñòâåííàÿ ñòðóêòóðà Bos taurus òèðîçèë-òÐÍÊ
ñèíòåòàçû ïðåäïîëàãàåò ñóùåñòâîâàíèå øàðíèðíîãî ìåõàíèçìà,
îáåñïå÷èâàåìîãî êîíñåðâàòèâíûì Gly353 â ìåæäîìåííîì ëèíêåðå
Ðåçþìå
Òèðîçèë-òÐÍÊ ñèíòåòàçà (TyrRS) ìëåêîïèòàþùèõ ñîñòîèò èç
äâóõ ñòðóêòóðíûõ ìîäóëåé: N-êîíöåâîãî êàòàëèòè÷åñêîãî ìîäó-
ëÿ (miniTyrRS) è íåêàòàëèòè÷åñêîãî öèòîêèí-ïîäîáíîãî C-êîíöå-
âîãî ìîäóëÿ, ñîåäèíåííûõ ãèáêèì ïåïòèäíûì ëèíêåðîì. Äî íàñòî-
ÿùåãî âðåìåíè ïðîñòðàíñòâåííàÿ ñòðóêòóðà ïîëíîðàçìåðíîé
TyrRS ìëåêîïèòàþùèõ íå ðåøåíà ìåòîäîì ðåíòãåíîâñêîé êðèñ-
òàëëîãðàôèè. Öåëü äàííîé ðàáîòû ñîñòîÿëà â ìîäåëèðîâàíèè ïî
ãîìîëîãèè ïðîñòðàíñòâåííîé ñòðóêòóðû ïîëíîðàçìåðíîé TyrRS
B. taurus. Ìåòîäû. Ìîäåëèðîâàíèå ïî ãîìîëîãèè TyrRS âûïîëíå-
íî ñ ïîìîùüþ ïàêåòà Modeller 9.1. Êà÷åñòâî ìîäåëåé îöåíèâàëè
ñ ïîìîùüþ Biotech Validation Suite web-ñåðâåðà. Ðåçóëüòàòû. Ïî
äàííûì BLAST-ïîèñêà îïðåäåëåíà 34 %-ÿ ãîìîëîãèÿ ïîñëåäîâà-
òåëüíîñòè ìåæäîìåííîãî ëèíêåðà TyrRS è ëèíêåðà c-Abl òèðî-
çèíêèíàçû ÷åëîâåêà. Äëÿ ìîäåëèðîâàíèÿ ñòðóêòóðû ïîëíîðàç-
ìåðíîé TyrRS, ìû ñîáðàëè ìîäåëü èç òðåõ ôðàãìåíòîâ áåëêà (N-
è Ñ-êîíöåâûõ äîìåíîâ è ìåæäîìåííîãî ëèíêåðà), èñïîëüçóÿ Mo-
deller 9.1. Ëó÷øàÿ ìîäåëü ñòðóêòóðû Abl-17 óòî÷íåíà ìåòîäîì
ìèíèìèçàöèè ýíåðãèè. Âûâîäû. Âûñîêàÿ ãèáêîñòü ìåæäîìåííî-
ãî ëèíêåðà ìîæåò ïðèâîäèòü ê ôîðìèðîâàíèþ ìíîæåñòâåííûõ
êîíôîðìàöèé TyrRS. Øàðíèðíûé ìåõàíèçì â ìåæäîìåííîì ëèí-
êåðå, âåðîÿòíî, îáåñïå÷èâàåòñÿ êîíñåðâàòèâíûì îñòàòêîì Gly
353. Ïðåäïîëàãàåòñÿ, ÷òî èç-çà âûñîêîé ãèáêîñòè ìåæäîìåííî-
ãî ëèíêåðà îòêðûòàÿ êîíôîðìàöèÿ TyrRS ìîæåò ïåðåõîäèòü â
çàêðûòóþ êîíôîðìàöèþ â ôåðìåíòíî-ñóáñòðàòíûõ êîìïëåêñàõ.
Êëþ÷åâûå ñëîâà: òèðîçèë-òÐÍÊ ñèíòåòàçà, ìîäåëèðîâàíèå
ïî ãîìîëîãèè, ìåæäîìåííûé ëèíêåð, c-Abl òèðîçèíêèíàçà, EMAP
II, òÐÍÊ
Tyr
.
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Received 25.07.12
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