the c-terminal region of human eukaryotic elongation ...ir.qibebt.ac.cn/bitstream/337004/8062/1/the...
TRANSCRIPT
NMR STRUCTURE NOTE
The C-terminal region of human eukaryotic elongation factor 1Bd
Huiwen Wu1 • Chen Wang2,3,4,5 • Weibin Gong1 • Jinfeng Wang1 • Jinsong Xuan5 •
Sarah Perrett1 • Yingang Feng2,3,4
Received: 29 October 2015 / Accepted: 6 January 2016 / Published online: 13 January 2016
� Springer Science+Business Media Dordrecht 2016
Biological context
In the elongation step of eukaryotic protein biosynthesis,
the eukaryotic elongation factor 1A (eEF1A) in its GTP-
bound active state transports the aminoacyl tRNA (aa-
tRNA) to the A site of the ribosome (Sasikumar et al.
2012). Correct codon–anticodon pairing induces hydrolysis
of GTP to GDP, which results in a conformational change
of eEF1A that causes its release from both the ribosome
and aa-tRNA. The eukaryotic elongation factor 1B
(eEF1B) complex containing 2–4 subunits helps to enhance
the intrinsically slow (*0.7 9 10-3/s) dissociation rate of
GDP from eEF1A by approximately 3000-fold and results
in GTP reloading and eEF1A reactivation (Janssen and
Moller 1988). The eEF1B complex is comprised of one or
two guanine nucleotide exchange factors (GEFs) (EF1Baexists in all eukaryotes, eEF1Bd exists only in metazoans,
and eEF1Bb exists only in plants), a scaffold component
named eEF1Bc, and a valine-tRNA synthetase (Val-RS)
additionally in metazoans (Le Sourd et al. 2006). Because
there is no structure of the eEF1B complex available,
several models have been proposed to explain the assembly
of the eEF1B complex in different species (Janssen et al.
1994; Sheu and Traugh 1997; Mansilla et al. 2002).
The GEFs of the eEF1B complex are the catalytic
components and each of them contain two regions (van
Damme et al. 1990; Wu et al. 2015): a less conserved
N-terminal region (Sanders et al. 1993) and a highly con-
served C-terminal region which comprises a central acidic
region, termed the CAR domain, and a C-terminal catalytic
GEF domain. The N-terminal region is mainly responsible
for interacting with eEF1Bc to facilitate assembly of the
eEF1B complex. In the C-terminal region, the GEF domain
is an essential catalytic domain, while the CAR domain is
not essential for the exchange activity. However, it was
found that the CAR domain may enhance the exchange
activity and regulates the GEF activity (Perez et al. 1998;
van Damme et al. 1991). The CAR domain contains the
casein kinase 2 (CK2) phosphorylation site (Sheu and
Traugh 1997) and has been shown to interact with trans-
lationally-controlled tumor protein (TCTP) which inhibits
the nucleotide-exchange activity of eEF1Bd (Wu et al.
2015; Cans et al. 2003). Even though the GEF and CAR
domains are highly conserved in eEF1Ba, eEF1Bb, and
eEF1Bd, evidence suggests that the regulation of their
Electronic supplementary material The online version of thisarticle (doi:10.1007/s10858-016-0012-6) contains supplementarymaterial, which is available to authorized users.
& Sarah Perrett
& Yingang Feng
1 National Laboratory of Biomacromolecules, Institute of
Biophysics, Chinese Academy of Sciences, Beijing 100101,
China
2 Qingdao Engineering Laboratory of Single Cell Oil, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese
Academy of Sciences, 189 Songling Road,
Qingdao 266101, Shandong, China
3 Shandong Key Laboratory of Synthetic Biology, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese
Academy of Sciences, 189 Songling Road,
Qingdao 266101, Shandong, China
4 CAS Key Laboratory of Biofuels, Qingdao Institute of
Bioenergy and Bioprocess Technology, Chinese Academy of
Sciences, 189 Songling Road, Qingdao 266101, Shandong,
China
5 Department of Biological Science and Engineering, School of
Chemical and Biological Engineering, University of Science
and Technology Beijing, Beijing 100083, China
123
J Biomol NMR (2016) 64:181–187
DOI 10.1007/s10858-016-0012-6
activity and the mechanism of binding to eEF1A could be
different. For example, human eEF1Ba but not eEF1Bdcan complement eEF1Ba-deficient yeasts (Carr-Schmid
et al. 1999); binding of eEF1A to eEF1Ba but not eEF1Bdresults in masking of the CK2 phosphorylation site (Sheu
and Traugh 1997); and the GEF activity of eEF1Ba but not
eEF1Bd increases after binding eEF1Bc (Bec et al. 1994).
The structures of the catalytic GEF domain of human
eEF1Ba (eEF1Ba GEF) and the yeast eEF1A-eEF1Ba GEF
domain complex have been reported (Perez et al. 1999;
Andersen et al. 2000, 2001). According to the reported
structures, eEF1Ba GEF is a two layered a/b sandwich
containing a b-sheet with four antiparallel strands and two
helices packing against one face of the b-sheet. The structure
of the yeast eEF1A-eEF1Ba GEF domain complex reveals
that eEF1A contains three domains (1, 2 and 3). One edge of
eEF1Ba GEF, which consists of N- and C- termini, interacts
with domain 1 of eEF1A, while the opposite edge of eEF1BaGEF interacts with domain 2 of eEF1A. The three residues at
the C-terminal end of eEF1Ba, especially the absolutely
conserved lysine residue, are essential for releasing GDP
from eEF1A, as it forms contacts with the domain 1 of
eEF1A at a Mg2? binding position, the displacement of
which triggers the release of nucleotide. However, a recent
crystallography study of human eEF1A2 suggests that the
exchange mechanism for human eEF1A may be different
and the Mg2? removal is dispensable for GDP binding and
dissociation (Crepin et al. 2014). The structure of the CAR
domain of human eEF1Bd was determined recently (Wu
et al. 2015). The CAR domain, containing an a-helix and
two flexible loops, is structurally independent of the GEF
domain as suggested by the interaction study. However,
neither the structure of the whole conserved C-terminal
region of eEF1B GEFs nor the structure of the GEF domain
of eEF1Bd or eEF1Bb is currently available.
Here, we report the NMR structures of the CAR and
GEF domains in the C-terminal region of human eEF1Bd.
Combined with the previously determined GEF structures,
the GEF domain structure of human eEF1Bd obtained here
was used for detailed structural comparisons of GEFs in
different species, in order to investigate the functions of
different domains of eEF1B GEFs.
Methods and results
Protein expression and purification
The gene construction, protein expression and purification
of human eEF1Bd CAR-GEF (residues 153–281 of
eEF1Bd) were performed following the procedures previ-
ously described (Wu et al. 2015). Briefly, the gene fragment
Table 1 Restraints and structure statistics of the 20 lowest energy
conformers of human eEF1Bd CAR-GEF
NOE restraints
Intra-residue 694
Sequential 424
Medium-range 234
Long-range 518
Ambiguous 1118
Total 2988
Hydrogen bond restraints 106
Torsion angle restraints
Phi (u) 101
Psi (w) 101
Chi1 (v1) 47
Violations
Max. NOE violation (A) 0.200
Max. torsion angle violation (�) 3.79
R.M.S.D. from mean structure (A)a
All residues of the GEF domain (residues 193–281)
Backbone heavy atoms 0.45 ± 0.10
All Heavy atoms 0.82 ± 0.06
Regular secondary structure residues of the GEF domainb
Backbone heavy atoms 0.31 ± 0.05
All heavy atoms 0.69 ± 0.05
All residues of the CAR domain (residues 153–192)
Backbone heavy atoms 7.12 ± 1.27
All heavy atoms 7.69 ± 1.23
Regular secondary structure residues of the CAR domainc
Backbone heavy atoms 0.49 ± 0.20
All heavy atoms 1.46 ± 0.17
Ramachandran statistics
Most favored region (%) 86.5
Additionally allowed (%) 11.1
Generously allowed (%) 1.0
Disallowed (%) 1.3d
WHAT_CHECK Z-scores
1st generation packing quality -0.823
2nd generation packing quality -1.546
Ramachandran plot appearance -2.630
Chi-1/chi-2 rotamer normality -1.838
Backbone conformation -1.346
Inside/outside distribution 1.128
a The structures were superposed by the backbone heavy atoms of
regular secondary structure regions of the corresponding domain
before calculating R.M.S.D of the GEF or CAR domainb Regular secondary structure regions of the GEF domain are resi-
dues 195–204, 211–219, 226–235, 241–250, 256–266, 270–280c Regular secondary structure regions of the CAR domain are resi-
dues 169–185d All the residues in disallowed regions of the Ramachandran plot are
located in the disordered N-terminal loop and the linker between the
CAR and GEF domains
182 J Biomol NMR (2016) 64:181–187
123
of human eEF1Bd CAR-GEF was cloned into a modified
pET28a expression vector and the protein was expressed in
Escherichia coli BL21 (DE3). Proteins were first purified by
affinity chromatography using a Ni2?-column (Chelating
Sepharose Fast Flow, GE Healthcare), and then were
digested with PreScission protease to remove the N-terminal
tag by passing through the Ni2?-column again. The fraction
containing eEF1Bd CAR-GEF was further purified using a
Superdex 75 gel filtration column (GE Healthcare).
NMR spectroscopy
Uniformly 15N- or 15N/13C-labeled human eEF1Bd CAR-
GEF was used in preparation of the NMR sample for dif-
ferent experiments. Human eEF1Bd CAR-GEF protein
(0.8 mM) was dissolved in 10 % (v/v) D2O containing
20 mM Tris–HCl buffer (pH 7.5), 200 mM NaCl, and
0.01 % 2,2-dimethyl-2-silapentane-5-sulfonate (DSS). All
NMR experiments were performed at 298 K on a Bruker
DMX 600 MHz NMR spectrometer equipped with a cryo-
probe. Two-dimensional 1H-15N and 1H-13C HSQC, and
three-dimensional CBCA(CO)NH, HNCACB, HNCO,
HN(CA)CO, HBHA(CO)NH, HBHANH, HCCH-TOCSY,
CCH-COSY, and CCH-TOCSY spectra were acquired for
backbone and side-chain resonance assignments. Distance
restraints were derived from three-dimensional 1H-15N and1H-13C NOESY-HSQC spectra collected with mixing times
of 150 ms. All data were processed with FELIX (Accelrys
Inc.) or NMRPipe (Delaglio et al. 1995) and analyzed with
NMRViewJ (Johnson and Blevins 1994).
Fig. 1 NMR structures of the
C-terminal region containing
the CAR and GEF domains of
human eEF1Bd (human
eEF1Bd CAR-GEF).
a Superposition of 20 lowest-
energy conformers for best
fitting to the backbone of the
CAR domain. b The same
superposition as in (a) for best
fitting to the backbone of the
GEF domain. c Ribbon
presentation of the structure of
human eEF1Bd CAR-GEF. The
secondary structure elements
are labeled. d Electrostatic
potential surface of the CAR
domain. The dashed curves
indicate the surfaces of
disordered regions which should
not be considered as defined
surfaces. e Electrostatic
potential surface of the GEF
domain. The CAR domain is
shown in blue and the GEF
domain in red (a, b, and c). In
the electrostatic surfaces, red is
negatively charged, and blue is
positively charged
J Biomol NMR (2016) 64:181–187 183
123
Structure calculations
The structures of human eEF1Bd CAR-GEF were initially
calculated with the program CYANA (Herrmann et al.
2002), and then refined using CNS (Brunger et al. 1998)
with semi-automated NOE assignments by SANE (Duggan
et al. 2001). Backbone u and w and side chain v1 dihedral
angle restraints obtained using TALOS-N (Shen and Bax
2013) and hydrogen-bond restraints according to the reg-
ular secondary structure patterns were also incorporated
into the late-stage structural calculation. The 50 lowest
energy conformers were selected from 100 initial structures
for refinement in explicit water using RECOORDScript
(Nederveen et al. 2005), and then the 20 lowest energy
structures were chosen to represent the final ensemble. The
quality of these structures was analyzed using the programs
MOLMOL (Koradi et al. 1996), PROCHECK-NMR
(Laskowski et al. 1996), and WHATCHECK (Hooft et al.
1996). PyMOL (Schrodinger, LCC) was used for visual-
ization of the structures. Atomic coordinates of the struc-
tures have been deposited in the PDB with accession code
2N51, and chemical shift assignments have been deposited
in the BioMagResBank under accession number 25690.
Solution structure of the C-terminal region
of human eEF1Bd
About 96.7 % of the 1H, 15N, and 13C resonances of the
backbone and side-chain atoms for human eEF1Bd CAR-
GEF were assigned. The assigned 1H-15N HSQC spectrum
is shown in Fig. S1. Based on the resonance assignments,
nearly 3000 NOEs were identified to generate distance
restraints for the structure calculations. However, no long
range NOEs between the CAR and GEF domains were
observed. The high quality of the final structural ensemble
of human eEF1Bd CAR-GEF was verified by statistical
analysis (Table 1). In Fig. 1a, b, the ensemble of structures
for each of the CAR and GEF domains are well superposed
when each domain is considered independently, and the
linking peptide segment between the two domains is dis-
ordered, showing that the two domains do not adopt a
unique orientation relative to each other. This suggests that
the CAR and GEF domains are structurally independent of
each other as reported previously (Wu et al. 2015). This is
further confirmed by the finding that the CAR and GEF
domains have different R2/R1 ratios in 15N backbone
relaxation measurements (Fig. S2).
The CAR domain (residues 153–192) contains one a-
helix (aCAR, residues 169–185) and two flexible loops on
either side of the helix (Fig. 1c). Although the NOE pat-
terns in the helix cannot be unambiguously verified
because of the severe overlap of the chemical shifts for
both HN and HA atoms in the helix, the helix is identified
by both chemical shift index (CSI) and TALOS-N pre-
diction from the chemical shifts (Fig. S3). The C-terminal
flexible loop represents a disordered region linking the
CAR and GEF domains. The electrostatic surface of the
CAR domain shows that the N-terminal flexible loop is
largely negatively charged while the C-terminal part of the
helix and the C-terminal flexible loop are mainly positively
charged (Fig. 1d). These structural features of the CAR
domain are essentially identical to those of the structure of
the standalone CAR domain reported in the previous study
(Wu et al. 2015), and the RMSD of backbone atoms in the
helices (residues 169–185) between the CAR domains of
the two structures is 0.73 ± 0.26 A. The GEF domain
(residues 193–281) contains an antiparallel four-strand b-
sheet (b1, 195–204; b2, 226–235; b3, 241–250; b4,
270–280) and two a-helices (a1, 211–219; a2, 256–266) in
the order b1–a1–b2–b3–a2–b4, which forms a typical two-
layer a/b sandwich structure (Fig. 1c). One side of the GEF
domain, including mainly the a2 and b4, is largely nega-
tively charged, while the other side is neutral and positively
charged (Fig. 1e).
Discussion and conclusions
The overall fold of the human eEF1Bd GEF domain is the
same as the previously reported structures of human and
yeast eEF1Ba GEF domains, which is expected as they
share high sequence homology (Fig. 2a). The human
eEF1Bd GEF domain (described here) and the eEF1BaGEF domain (PDB code 1B64) superimpose with an
RMSD of 1.6 A, indicating significant similarity between
the domains. Differences occur mainly in the flexible loops
and the boundary of secondary structural elements
(Fig. 2b), which is likely due to the fluctuation of solution
NMR structures. Although the domains show conserved
structural features, they do not share all conserved salt
bridges. Each domain has a salt bridge, which is between
residues E262 and K265 within the helix a2 of the eEF1BdGEF domain and residues K157 and E160 within the helix
a1 of the eEF1Ba GEF domain. However, the corre-
sponding residues are Q206 and A209 in the eEF1Ba GEF
domain, and Q213 and A216 in the eEF1Bd GEF domain.
The salt bridge formed by the non-conserved residues in
helix a2 of the domains may induce about one additional
turn in the helix a2 of the eEF1Bd GEF domain compared
to the eEF1Ba GEF domain (Fig. 2c). Nevertheless, no
significant backbone difference of the a1 helices is
observed (Fig. 2c). Since the GEF domain represents a
two-layer a/b sandwich structure (Fig. 1c), and the b-sheet
is responsible for binding to eEF1A, it is not clear whether
the non-conservation of the salt bridges in the helices has
any functional significance.
184 J Biomol NMR (2016) 64:181–187
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Superposition of the structures of the human eEF1BdGEF domain with the previously determined yeast eEF1BaGEF domain in the eEF1Ba-eEF1A complex (PDB code
1IJF) gives an RMSD of 1.3 A, revealing a highly
conserved overall fold (Fig. 2d, e). Residues involved in
catalysis and contact with eEF1A of the yeast eEF1BaGEF in the complex are highly conserved in the human
eEF1Bd and eEF1Ba GEF domains in term of sequence
Fig. 2 Structure comparison of human eEF1Bd CAR-GEF with
known eEF1B structures. a Sequence alignment of the CAR-GEFs of
human eEF1Bd, human eEF1Ba, and yeast eEF1Ba. Secondary
structure elements of human eEF1Bd CAR-GEF are shown above the
sequence. The residues in yeast eEF1Ba that contact eEF1A in the
eEF1A-eEF1Ba complex are indicated by stars below the sequence.
b Superposition of a representative set of the NMR structures of
human eEF1Bd GEF domain (red) onto human eEF1Ba GEF domain
(PDB code 1B64, cyan). c The salt bridges formed within the helices
of human eEF1Bd GEF domain (red) and human eEF1Ba GEF
domain (PDB code 1B64, cyan). Residues are shown as sticks colored
by atom types (carbon in green, oxygen in red, and nitrogen in blue).
d Superposition of the NMR structure of human eEF1Bd GEF domain
(red) onto the crystal structure of yeast eEF1Ba GEF domain (PDB
code 1IJF, green). The residues in yeast eEF1Ba that contact eEF1A
and the corresponding residues in human eEF1Bd are shown as sticks.
e Superposition of the NMR structure of human eEF1Bd CAR-GEF
onto the crystal structure of the yeast eEF1Ba-eEF1A complex (PDB
code 1IJF). The human eEF1Bd CAR domain, the human eEF1BdGEF domain, the yeast eEF1Ba GEF domain, and the yeast eEF1A
are colored in blue, red, green, and grey, respectively. GDP is shown
as orange sticks, and Mg2? is shown as a magenta ball
J Biomol NMR (2016) 64:181–187 185
123
and structure. These residues are located on two edges of
the antiparallel four-strand b-sheet (Fig. 2d). On one edge,
the contacting residues include the absolutely conserved
residues K128, P160, I165, Q196, and D199 at the C-ter-
mini of b1 and b2 and the N-termini of b3 and b4, as well as
the similar hydrophobic residues F163 and Y238 in the
human and yeast GEF domains, respectively, in the loop
between b1 and b2 (Fig. 2d). On the opposite edge of the b-
sheet, a group of conserved residues at the C-terminus of
b4, including the absolutely conserved residue K205 (K280
in yeast eEF1Ba), similar hydrophobic residues M203 and
L206 (F276 and I281 in yeast eEF1Ba), and similar glu-
tamine residue Q204 (N279 in yeast eEF1Ba) (Fig. 2d), are
involved in the interaction with eEF1A. This similarity
suggests that the modes of binding between different
eEF1B GEFs and eEF1A are essentially the same in
humans and yeast, and the different eEF1B GEFs may
share the same catalytic mechanism for GEF activity, that
is the C-terminal lysine residue of the eEF1B GEF domain
disrupts the interaction of Mg2? with eEF1A, resulting in
the release of GDP from eEF1A (Andersen et al. 2000,
2001). However, a recent study describing the crystal
structure of human eEF1A2 proposed a different exchange
mechanism for human eEF1A, namely that the conforma-
tional change induced by eEF1B binding plays a critical
role, rather than the Mg2? removal step (Crepin et al.
2014). As shown in the present structure comparison
(Fig. 2d), residues adjacent to the C-terminal lysine residue
in human eEF1Ba and eEF1Bd are similar but not identical
to those in yeast eEF1Ba. Presumably, the position and
conformation of the catalytic lysine of human eEF1Ba and
eEF1Bd may be slightly different from that of yeast
eEF1Ba when they bind to eEF1A, which might make the
Mg2? dispensable for GDP binding and dissociation.
In the antiparallel four-strand b-sheet of the GEF
domain, the C-terminal catalytic lysine residue is adjacent
to the N-terminus of the b1 strand of the GEF domain
(Fig. 2d). Since the CAR domain connects to the N-ter-
minus of the b1 strand of the GEF domain (Fig. 1c), such
an arrangement should form a basis for the regulatory role
of the CAR domain for the GEF activity reported previ-
ously (van Damme et al. 1991; Perez et al. 1998; Cans et al.
2003; Wu et al. 2015). Superposition of the human eEF1BdCAR-GEF structure onto the crystal structure of the yeast
eEF1Ba-eEF1A complex (Andersen et al. 2001) indicates
that the position of the CAR domain will be restricted to
some extent in the vicinity of the nucleotide binding pocket
of eEF1A when eEF1Bd and eEF1A form a complex
(Fig. 2e), which is probably the structural basis of the
regulation function of some CAR-domain binding proteins
such as TCTP (Wu et al. 2015). However, this cannot
exclude the possibility that the CAR domain also interacts
with eEF1A in the eEF1Bd-eEF1A complex to play a
regulatory role, because the linker between the CAR
domain and the GEF domain is flexible. If this is true, not
only the steric hindrance but also the disruption of the
interaction between the CAR domain and eEF1A could be
the mechanism of the guanine nucleotide dissociation
inhibitor activity of TCTP. Although clarification of the
functional role of the CAR domain needs further study, the
structure of human eEF1Bd CAR-GEF described here
provides a structural basis for understanding the guanine
nucleotide exchange function of eEF1Bd.
Acknowledgments This work was supported by the National Basic
Research Program from Ministry of Science and Technology of China
(973 Program, Grant Nos. 2012CB911000 and 2013CB910700 to
S.P.), the National High-tech R&D Program from Ministry of Science
and Technology of China (863 Program, Grant No. 2012AA02A707
to Y.F.), and the National Natural Science Foundation of China
(30800179 and 31170701 to Y.F.; 31300635 to J.X.; 31200578 and
31470747 to W.G.; and 31110103914 to S.P.).
Compliance with ethical standards
Conflict of interest The authors declare no conflict of interest.
Ethical standard Research does not involve human participants
and/or animals.
References
Andersen GR, Pedersen L, Valente L, Chatterjee I, Kinzy TG,
Kjeldgaard M, Nyborg J (2000) Structural basis for nucleotide
exchange and competition with tRNA in the yeast elongation
factor complex eEF1A:eEF1Ba. Mol Cell 6(5):1261–1266.
doi:10.1016/S1097-2765(00)00122-2
Andersen GR, Valente L, Pedersen L, Kinzy TG, Nyborg J (2001)
Crystal structures of nucleotide exchange intermediates in the
eEF1A-eEF1Ba complex. Nat Struct Biol 8(6):531–534. doi:10.
1038/88598
Bec G, Kerjan P, Waller JP (1994) Reconstitution in vitro of the
valyl-tRNA synthetase-elongation factor (EF) 1 bcd complex.
J Biol Chem 269(3):2086–2092
Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-
Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS,
Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallog-
raphy and NMR system: a new software suite for macromolec-
ular structure determination. Acta Crystallogr Sect D Biol
Crystallogr 54:905–921. doi:10.1107/S0907444998003254
Cans C, Passer BJ, Shalak V, Nancy-Portebois V, Crible V, Amzallag
N, Allanic D, Tufino R, Argentini M, Moras D, Fiucci G, Goud
B, Mirande M, Amson R, Telerman A (2003) Translationally
controlled tumor protein acts as a guanine nucleotide dissocia-
tion inhibitor on the translation elongation factor eEF1A. Proc
Natl Acad Sci USA 100(24):13892–13897. doi:10.1073/pnas.
2335950100
Carr-Schmid A, Valente L, Loik VI, Williams T, Starita LM, Kinzy
TG (1999) Mutations in elongation factor 1b, a guanine
nucleotide exchange factor, enhance translational fidelity. Mol
Cell Biol 19(8):5257–5266. doi:10.1128/MCB.19.8.5257
Crepin T, Shalak VF, Yaremchuk AD, Vlasenko DO, McCarthy A,
Negrutskii BS, Tukalo MA, El’skaya AV (2014) Mammalian
186 J Biomol NMR (2016) 64:181–187
123
translation elongation factor eEF1A2: X-ray structure and new
features of GDP/GTP exchange mechanism in higher eukaryotes.
Nucleic Acids Res 42(20):12939–12948. doi:10.1093/nar/
gku974
Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995)
NMRPipe: a multidimensional spectral processing system based
on UNIX pipes. J Biomol NMR 6(3):277–293. doi:10.1007/
BF00197809
Duggan BM, Legge GB, Dyson HJ, Wright PE (2001) SANE
(structure assisted NOE evaluation): an automated model-based
approach for NOE assignment. J Biomol NMR 19(4):321–329.
doi:10.1023/A:1011227824104
Herrmann T, Guntert P, Wuthrich K (2002) Protein NMR structure
determination with automated NOE assignment using the new
software CANDID and the torsion angle dynamics algorithm
DYANA. J Mol Biol 319(1):209–227. doi:10.1016/S0022-
2836(02)00241-3
Hooft RW, Vriend G, Sander C, Abola EE (1996) Errors in protein
structures. Nature 381(6580):272. doi:10.1038/381272a0
Janssen GM, Moller W (1988) Kinetic studies on the role of
elongation factors 1b and 1c in protein synthesis. J Biol Chem
263(4):1773–1778
Janssen GM, van Damme HT, Kriek J, Amons R, Moller W (1994)
The subunit structure of elongation factor 1 from Artemia. J Biol
Chem 269(50):31410–31417
Johnson BA, Blevins RA (1994) NMRView: a computer program for
the visualization and analysis of NMR data. J Biomol NMR
4(5):603–614. doi:10.1007/BF00404272
Koradi R, Billeter M, Wuthrich K (1996) MOLMOL: a program for
display and analysis of macromolecular structures. J Mol
Graph 14(1):51–55, 29–32. doi:10.1016/0263-7855(96)00009-4
Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton
JM (1996) AQUA and PROCHECK-NMR: programs for
checking the quality of protein structures solved by NMR.
J Biomol NMR 8(4):477–486. doi:10.1007/BF00228148
Le Sourd F, Boulben S, Le Bouffant R, Cormier P, Morales J, Belle
R, Mulner-Lorillon O (2006) eEF1B: at the dawn of the 21st
century. Biochim Biophys Acta 1759(1–2):13–31. doi:10.1016/j.
bbaexp.2006.02.003
Mansilla F, Friis I, Jadidi M, Nielsen KM, Clark BF, Knudsen CR
(2002) Mapping the human translation elongation factor eEF1H
complex using the yeast two-hybrid system. Biochem J
365(3):669–676. doi:10.1042/BJ20011681
Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CA,
Nabuurs SB, Guntert P, Livny M, Markley JL, Nilges M, Ulrich
EL, Kaptein R, Bonvin AM (2005) RECOORD: a recalculated
coordinate database of 500 ? proteins from the PDB using
restraints from the BioMagResBank. Proteins 59(4):662–672.
doi:10.1002/prot.20408
Perez JM, Kriek J, Dijk J, Canters GW, Moller W (1998) Expression,
purification, and spectroscopic studies of the guanine nucleotide
exchange domain of human elongation factor, EF-1b. Protein
Expr Purif 13(2):259–267. doi:10.1006/prep.1998.0895
Perez JM, Siegal G, Kriek J, Hard K, Dijk J, Canters GW, Moller W
(1999) The solution structure of the guanine nucleotide exchange
domain of human elongation factor 1b reveals a striking
resemblance to that of EF-Ts from Escherichia coli. Struc-
ture 7(2):217–226. doi:10.1016/S0969-2126(99)80027-6
Sanders J, Raggiaschi R, Morales J, Moller W (1993) The human
leucine zipper-containing guanine-nucleotide exchange protein
elongation factor-1d. Biochim Biophys Acta 1174(1):87–90.
doi:10.1016/0167-4781(93)90097-W
Sasikumar AN, Perez WB, Kinzy TG (2012) The many roles of the
eukaryotic elongation factor 1 complex. WIREs RNA
3(4):543–555. doi:10.1002/wrna.1118
Shen Y, Bax A (2013) Protein backbone and sidechain torsion angles
predicted from NMR chemical shifts using artificial neural networks.
J Biomol NMR 56(3):227–241. doi:10.1007/s10858-013-9741-y
Sheu GT, Traugh JA (1997) Recombinant subunits of mammalian
elongation factor 1 expressed in Escherichia coli. J Biol Chem
272(52):33290–33297. doi:10.1074/jbc.272.52.33290
van Damme HT, Amons R, Karssies R, Timmers CJ, Janssen GM, Moller
W (1990) Elongation factor 1b of artemia: localization of functional
sites and homology to elongation factor 1d. Biochim Biophys Acta
1050(1–3):241–247. doi:10.1016/0167-4781(90)90174-
van Damme H, Amons R, Janssen G, Moller W (1991) Mapping the
functional domains of the eukaryotic elongation factor 1bc. Eur J
Biochem 197(2):505–511. doi:10.1111/j.1432-1033.1991.tb15938.x
Wu H, Gong W, Yao X, Wang J, Perrett S, Feng Y (2015)
Evolutionarily conserved binding of translationally-controlled
tumor protein to eukaryotic elongation factor 1B. J Biol Chem.
doi:10.1074/jbc.M114.628594
J Biomol NMR (2016) 64:181–187 187
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