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PDBsum entry 1etu
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Transport and protection protein
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PDB id
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1etu
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Contents |
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* Residue conservation analysis
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Embo J
4:2385-2388
(1985)
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PubMed id:
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Structural details of the binding of guanosine diphosphate to elongation factor Tu from E. coli as studied by X-ray crystallography.
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T.F.la Cour,
J.Nyborg,
S.Thirup,
B.F.Clark.
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ABSTRACT
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Structural details of the guanosine diphosphate binding to a modified form of
elongation factor Tu from Escherichia coli, resulting from X-ray
crystallographic studies, are reported. The protein elements that take part in
the nucleotide binding are located in four loops connecting beta-strands with
alpha-helices. These loops correspond to regions in primary sequences which show
a high degree of homology when compared with other prokaryotic and eukaryotic
elongation factors and initiation factor 2.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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D.Guymer,
J.Maillard,
M.F.Agacan,
C.A.Brearley,
and
F.Sargent
(2010).
Intrinsic GTPase activity of a bacterial twin-arginine translocation proofreading chaperone induced by domain swapping.
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FEBS J,
277,
511-525.
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X.Agirrezabala,
and
J.Frank
(2009).
Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu.
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Q Rev Biophys,
42,
159-200.
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L.Qiu,
S.Jiang,
F.Zhou,
D.Zhang,
J.Huang,
and
Y.Guo
(2008).
Molecular cloning of the black tiger shrimp (Penaeus monodon) elongation factor 2 (EF-2): sequence analysis and its expression on the ovarian maturation stage.
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Mol Biol Rep,
35,
431-438.
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N.G.Abdulaev,
T.Ngo,
C.Zhang,
A.Dinh,
D.M.Brabazon,
K.D.Ridge,
and
J.P.Marino
(2005).
Heterotrimeric G-protein alpha-subunit adopts a "preactivated" conformation when associated with betagamma-subunits.
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J Biol Chem,
280,
38071-38080.
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C.M.Carvalho,
J.Pouwels,
J.W.van Lent,
T.Bisseling,
R.W.Goldbach,
and
J.Wellink
(2004).
The movement protein of cowpea mosaic virus binds GTP and single-stranded nucleic acid in vitro.
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J Virol,
78,
1591-1594.
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A.Carr-Schmid,
C.Pfund,
E.A.Craig,
and
T.G.Kinzy
(2002).
Novel G-protein complex whose requirement is linked to the translational status of the cell.
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Mol Cell Biol,
22,
2564-2574.
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E.Schmitt,
S.Blanquet,
and
Y.Mechulam
(2002).
The large subunit of initiation factor aIF2 is a close structural homologue of elongation factors.
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EMBO J,
21,
1821-1832.
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PDB codes:
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V.Chazalet,
K.Uehara,
R.A.Geremia,
and
C.Breton
(2001).
Identification of essential amino acids in the Azorhizobium caulinodans fucosyltransferase NodZ.
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J Bacteriol,
183,
7067-7075.
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C.F.Huang,
and
N.N.Chuang
(2000).
Disrupting the geranylgeranylation at the C-termini of the shrimp Ras by depriving guanine nucleotide binding at the N-terminal.
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J Exp Zool,
286,
441-449.
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D.Fagegaltier,
N.Hubert,
K.Yamada,
T.Mizutani,
P.Carbon,
and
A.Krol
(2000).
Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation.
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EMBO J,
19,
4796-4805.
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J.R.Walker,
C.Hervas,
J.D.Ross,
A.Blinkova,
M.J.Walbridge,
E.J.Pumarega,
M.O.Park,
and
H.R.Neely
(2000).
Escherichia coli DNA polymerase III tau- and gamma-subunit conserved residues required for activity in vivo and in vitro.
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J Bacteriol,
182,
6106-6113.
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S.Meunier,
R.Spurio,
M.Czisch,
R.Wechselberger,
M.Guenneugues,
C.O.Gualerzi,
and
R.Boelens
(2000).
Structure of the fMet-tRNA(fMet)-binding domain of B. stearothermophilus initiation factor IF2.
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EMBO J,
19,
1918-1926.
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PDB code:
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A.Carr-Schmid,
N.Durko,
J.Cavallius,
W.C.Merrick,
and
T.G.Kinzy
(1999).
Mutations in a GTP-binding motif of eukaryotic elongation factor 1A reduce both translational fidelity and the requirement for nucleotide exchange.
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J Biol Chem,
274,
30297-30302.
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S.Luchin,
H.Putzer,
J.W.Hershey,
Y.Cenatiempo,
M.Grunberg-Manago,
and
S.Laalami
(1999).
In vitro study of two dominant inhibitory GTPase mutants of Escherichia coli translation initiation factor IF2. Direct evidence that GTP hydrolysis is necessary for factor recycling.
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J Biol Chem,
274,
6074-6079.
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I.Majerfeld,
and
M.Yarus
(1998).
Isoleucine:RNA sites with associated coding sequences.
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RNA,
4,
471-478.
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M.Yamauchi,
and
T.A.Baker
(1998).
An ATP-ADP switch in MuB controls progression of the Mu transposition pathway.
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EMBO J,
17,
5509-5518.
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S.Guo,
and
D.H.Ives
(1998).
Functional assignment by Chimera construction of the domain affecting heterotropic activation of deoxyadenosine kinase from Lactobacillus acidophilus R-26.
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J Biol Chem,
273,
26624-26630.
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Y.Weng,
K.Czaplinski,
and
S.W.Peltz
(1998).
ATP is a cofactor of the Upf1 protein that modulates its translation termination and RNA binding activities.
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RNA,
4,
205-214.
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B.Yu,
V.Z.Slepak,
and
M.I.Simon
(1997).
Characterization of a Goalpha mutant that binds xanthine nucleotides.
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J Biol Chem,
272,
18015-18019.
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J.Osuna,
X.Soberón,
and
E.Morett
(1997).
A proposed architecture for the central domain of the bacterial enhancer-binding proteins based on secondary structure prediction and fold recognition.
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Protein Sci,
6,
543-555.
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K.L.Graves-Woodward,
J.Gottlieb,
M.D.Challberg,
and
S.K.Weller
(1997).
Biochemical analyses of mutations in the HSV-1 helicase-primase that alter ATP hydrolysis, DNA unwinding, and coupling between hydrolysis and unwinding.
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J Biol Chem,
272,
4623-4630.
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S.R.Sprang
(1997).
G protein mechanisms: insights from structural analysis.
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Annu Rev Biochem,
66,
639-678.
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A.Wittinghofer
(1996).
Deciphering the alphabet of G proteins: the structure of the alpha, beta, gamma heterotrimer.
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Structure,
4,
357-361.
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D.V.Quon,
M.G.Delgadillo,
and
P.J.Johnson
(1996).
Transcription in the early diverging eukaryote Trichomonas vaginalis: an unusual RNA polymerase II and alpha-amanitin-resistant transcription of protein-coding genes.
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J Mol Evol,
43,
253-262.
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E.M.Zera,
D.P.Molloy,
J.K.Angleson,
J.B.Lamture,
T.G.Wensel,
and
J.A.Malinski
(1996).
Low affinity interactions of GDPbetaS and ribose- or phosphoryl-substituted GTP analogues with the heterotrimeric G protein, transducin.
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J Biol Chem,
271,
12925-12931.
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I.V.Turko,
T.L.Haik,
L.M.McAllister-Lucas,
F.Burns,
S.H.Francis,
and
J.D.Corbin
(1996).
Identification of key amino acids in a conserved cGMP-binding site of cGMP-binding phosphodiesterases. A putative NKXnD motif for cGMP binding.
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J Biol Chem,
271,
22240-22244.
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K.A.Maegley,
S.J.Admiraal,
and
D.Herschlag
(1996).
Ras-catalyzed hydrolysis of GTP: a new perspective from model studies.
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Proc Natl Acad Sci U S A,
93,
8160-8166.
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K.Abel,
and
F.Jurnak
(1996).
A complex profile of protein elongation: translating chemical energy into molecular movement.
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Structure,
4,
229-238.
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R.C.Pillutla,
J.Ahnn,
and
M.Inouye
(1996).
Deletion of the putative effector region of Era, an essential GTP-binding protein in Escherichia coli, causes a dominant-negative phenotype.
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FEMS Microbiol Lett,
143,
47-55.
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Y.Weng,
K.Czaplinski,
and
S.W.Peltz
(1996).
Genetic and biochemical characterization of mutations in the ATPase and helicase regions of the Upf1 protein.
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Mol Cell Biol,
16,
5477-5490.
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C.Desbiez,
C.David,
A.Mettouchi,
J.Laufs,
and
B.Gronenborn
(1995).
Rep protein of tomato yellow leaf curl geminivirus has an ATPase activity required for viral DNA replication.
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Proc Natl Acad Sci U S A,
92,
5640-5644.
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C.R.Knudsen,
I.V.Kjaersgård,
O.Wiborg,
and
B.F.Clark
(1995).
Mutation of the conserved Gly94 and Gly126 in elongation factor Tu from Escherichia coli. Elucidation of their structural and functional roles.
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Eur J Biochem,
228,
176-183.
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D.G.Brown,
R.Visse,
G.Sandhu,
A.Davies,
P.J.Rizkallah,
C.Melitz,
W.C.Summers,
and
M.R.Sanderson
(1995).
Crystal structures of the thymidine kinase from herpes simplex virus type-1 in complex with deoxythymidine and ganciclovir.
|
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Nat Struct Biol,
2,
876-881.
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PDB code:
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D.W.Deerfield,
D.J.Fox,
M.Head-Gordon,
R.G.Hiskey,
and
L.G.Pedersen
(1995).
The first solvation shell of magnesium ion in a model protein environment with formate, water, and X-NH3, H2S, imidazole, formaldehyde, and chloride as ligands: an Ab initio study.
|
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Proteins,
21,
244-255.
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E.S.Yaskowiak,
and
P.E.March
(1995).
Small clusters of divergent amino acids surrounding the effector domain mediate the varied phenotypes of EF-G and LepA expression.
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Mol Microbiol,
15,
943-953.
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J.M.Zhong,
M.C.Chen-Hwang,
and
Y.W.Hwang
(1995).
Switching nucleotide specificity of Ha-Ras p21 by a single amino acid substitution at aspartate 119.
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J Biol Chem,
270,
10002-10007.
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M.Schwemmle,
M.F.Richter,
C.Herrmann,
N.Nassar,
and
P.Staeheli
(1995).
Unexpected structural requirements for GTPase activity of the interferon-induced MxA protein.
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J Biol Chem,
270,
13518-13523.
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M.V.Rodnina,
R.Fricke,
L.Kuhn,
and
W.Wintermeyer
(1995).
Codon-dependent conformational change of elongation factor Tu preceding GTP hydrolysis on the ribosome.
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EMBO J,
14,
2613-2619.
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T.Samuelsson,
M.Olsson,
P.M.Wikström,
and
B.R.Johansson
(1995).
The GTPase activity of the Escherichia coli Ffh protein is important for normal growth.
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Biochim Biophys Acta,
1267,
83-91.
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V.L.Woriax,
W.Burkhart,
and
L.L.Spremulli
(1995).
Cloning, sequence analysis and expression of mammalian mitochondrial protein synthesis elongation factor Tu.
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Biochim Biophys Acta,
1264,
347-356.
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A.Haug,
B.Shi,
and
V.Vitorello
(1994).
Aluminum interaction with phosphoinositide-associated signal transduction.
|
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Arch Toxicol,
68,
1-7.
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I.Majerfeld,
and
M.Yarus
(1994).
An RNA pocket for an aliphatic hydrophobe.
|
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Nat Struct Biol,
1,
287-292.
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J.S.Schwedock,
C.Liu,
T.S.Leyh,
and
S.R.Long
(1994).
Rhizobium meliloti NodP and NodQ form a multifunctional sulfate-activating complex requiring GTP for activity.
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J Bacteriol,
176,
7055-7064.
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L.G.Ofverstedt,
K.Zhang,
S.Tapio,
U.Skoglund,
and
L.A.Isaksson
(1994).
Starvation in vivo for aminoacyl-tRNA increases the spatial separation between the two ribosomal subunits.
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Cell,
79,
629-638.
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R.Ye,
S.N.Rehemtulla,
and
S.L.Wong
(1994).
Glucitol induction in Bacillus subtilis is mediated by a regulatory factor, GutR.
|
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J Bacteriol,
176,
3321-3327.
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S.D.Rufino,
and
T.L.Blundell
(1994).
Structure-based identification and clustering of protein families and superfamilies.
|
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J Comput Aided Mol Des,
8,
5.
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S.Laalami,
A.V.Timofeev,
H.Putzer,
J.Leautey,
and
M.Grunberg-Manago
(1994).
In vivo study of engineered G-domain mutants of Escherichia coli translation initiation factor IF2.
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Mol Microbiol,
11,
293-302.
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T.Schweins,
and
A.Wittinghofer
(1994).
GTP-binding proteins. Structures, interactions and relationships.
|
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Curr Biol,
4,
547-550.
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T.W.Traut
(1994).
The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide-binding sites.
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Eur J Biochem,
222,
9.
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W.R.Taylor,
T.P.Flores,
and
C.A.Orengo
(1994).
Multiple protein structure alignment.
|
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Protein Sci,
3,
1858-1870.
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C.Barker,
A.Makris,
C.Patriotis,
S.E.Bear,
and
P.N.Tsichlis
(1993).
Identification of the gene encoding the mitochondrial elongation factor G in mammals.
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Nucleic Acids Res,
21,
2641-2647.
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I.Tubulekas,
and
D.Hughes
(1993).
A single amino acid substitution in elongation factor Tu disrupts interaction between the ternary complex and the ribosome.
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J Bacteriol,
175,
240-250.
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J.F.Eccleston,
D.P.Molloy,
M.G.Hinds,
R.W.King,
and
J.Feeney
(1993).
Conformational differences between complexes of elongation factor Tu studied 19F-NMR spectroscopy.
|
| |
Eur J Biochem,
218,
1041-1047.
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J.Muñoz-Dorado,
N.Almaula,
S.Inouye,
and
M.Inouye
(1993).
Autophosphorylation of nucleoside diphosphate kinase from Myxococcus xanthus.
|
| |
J Bacteriol,
175,
1176-1181.
|
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M.Kjeldgaard,
P.Nissen,
S.Thirup,
and
J.Nyborg
(1993).
The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation.
|
| |
Structure,
1,
35-50.
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PDB code:
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G.A.Gentry
(1992).
Viral thymidine kinases and their relatives.
|
| |
Pharmacol Ther,
54,
319-355.
|
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|
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L.A.Zhu,
and
S.K.Weller
(1992).
The six conserved helicase motifs of the UL5 gene product, a component of the herpes simplex virus type 1 helicase-primase, are essential for its function.
|
| |
J Virol,
66,
469-479.
|
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M.Y.Mistou,
R.H.Cool,
and
A.Parmeggiani
(1992).
Effects of ions on the intrinsic activities of c-H-ras protein p21. A comparison with elongation factor Tu.
|
| |
Eur J Biochem,
204,
179-185.
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P.H.Anborgh,
A.Parmeggiani,
and
J.Jonák
(1992).
Site-directed mutagenesis of elongation factor Tu. The functional and structural role of residue Cys81.
|
| |
Eur J Biochem,
208,
251-257.
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P.J.Rapiejko,
and
R.Gilmore
(1992).
Protein translocation across the ER requires a functional GTP binding site in the alpha subunit of the signal recognition particle receptor.
|
| |
J Cell Biol,
117,
493-503.
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R.H.Voss,
R.K.Hartmann,
C.Lippmann,
C.Alexander,
O.Jahn,
and
V.A.Erdmann
(1992).
Sequence of the tufA gene encoding elongation factor EF-Tu from Thermus aquaticus and overproduction of the protein in Escherichia coli.
|
| |
Eur J Biochem,
207,
839-846.
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R.Martinez,
L.Shao,
and
S.K.Weller
(1992).
The conserved helicase motifs of the herpes simplex virus type 1 origin-binding protein UL9 are important for function.
|
| |
J Virol,
66,
6735-6746.
|
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W.C.Merrick
(1992).
Mechanism and regulation of eukaryotic protein synthesis.
|
| |
Microbiol Rev,
56,
291-315.
|
|
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|
|
|
A.Wittinghofer,
and
E.F.Pai
(1991).
The structure of Ras protein: a model for a universal molecular switch.
|
| |
Trends Biochem Sci,
16,
382-387.
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C.C.Hall,
J.D.Watkins,
and
N.H.Georgopapadakou
(1991).
Comparison of the Tu elongation factors from Staphylococcus aureus and Escherichia coli: possible basis for elfamycin insensitivity.
|
| |
Antimicrob Agents Chemother,
35,
2366-2370.
|
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C.Sander,
and
R.Schneider
(1991).
Database of homology-derived protein structures and the structural meaning of sequence alignment.
|
| |
Proteins,
9,
56-68.
|
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D.Doyle,
K.J.McDowall,
M.J.Butler,
and
I.S.Hunter
(1991).
Characterization of an oxytetracycline-resistance gene, otrA, of Streptomyces rimosus.
|
| |
Mol Microbiol,
5,
2923-2933.
|
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F.Quan,
L.Thomas,
and
M.Forte
(1991).
Drosophila stimulatory G protein alpha subunit activates mammalian adenylyl cyclase but interacts poorly with mammalian receptors: implications for receptor-G protein interaction.
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from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
