BRENDA - Enzyme Database show
show all sequences of 3.6.5.4

Molecular mechanism of GTPase activation at the signal recognition particle (SRP) RNA distal end

Shen, K.; Wang, Y.; Hwang Fu, Y.H.; Zhang, Q.; Feigon, J.; Shan, S.O.; J. Biol. Chem. 288, 36385-36397 (2013)

Data extracted from this reference:

Activating Compound
Activating Compound
Commentary
Organism
Structure
signal recognition particle RNA
SRP RNA, the signal recognition particle RNA distal end triggers GTP hydrolysis in the signal recognition particle protein-SRP receptor GTPase, i.e. Ffh-FtsY GTPase, complex. An intact docking site at the distal end of SRP RNA is required to stimulate GTPase activation. Loop E plays a crucial role in GTPase activation by the SRP RNA
Escherichia coli
Engineering
Amino acid exchange
Commentary
Organism
C86A
mutations at C86 yield a more complex pattern: whereas C86A and C86U completely abolish GTPase activation by the RNA, C86 and C86G reduce GTPase activity by only 50%
Escherichia coli
C86G
mutations at C86 yield a more complex pattern: whereas C86A and C86U completely abolish GTPase activation by the RNA, DELTAC86 and C86G reduce GTPase activity by only 50%. Despite defective GTP hydrolysis, the G83A mutant shows any detectable defect in the efficiency of GTPase docking at the distal end
Escherichia coli
C86U
mutations at C86 yield a more complex pattern: whereas C86A and C86U completely abolish GTPase activation by the RNA, C86 and C86G reduce GTPase activity by only 50%
Escherichia coli
C87A/C97U
site-directed mutagenesis, combining C97U with C87A generates a superactive SRP RNA double mutant that hydrolyzes GTP 5.5fold faster than wild-type SRP RNA
Escherichia coli
C97U
site-directed mutagenesis, the mutant prolongs GTPase docking at the distal end, which correlates with its faster GTP hydrolysis rate
Escherichia coli
C97U/G99A
site-directed mutagenesis, combining G99A with C87A generate s a superactive SRP RNA double mutant that hydrolyzes GTP 4.6fold faster than wild-type SRP RNA
Escherichia coli
G83A
deletion or substitution of G83 by any other nucleotide completely abolishes the stimulatory effect of the SRP RNA on GTP hydrolysis. Despite defective GTP hydrolysis, the G83A mutant shows any detectable defect in the efficiency of GTPase docking at the distal end
Escherichia coli
G99A
site-directed mutagenesis, the mutant prolongs GTPase docking at the distal end, which correlates with its faster GTP hydrolysis rate
Escherichia coli
additional information
several mutants show higher GTPase activity than wild-type SRP RNA, most notably mutations at G99, U12, and C97. By modifying the GTPase docking interface, the efficiency of activation of the Ffh-FtsY GTPase complex can be specifically tuned. When G83 is mutated, substitution of C86 with guanine rescues the SRP RNA-mediated stimulation of GTPase activity to 50% of wild-type rate. Despite defective GTP hydrolysis, neither the G83A nor C86G mutant shows any detectable defect in the efficiency of GTPase docking at the distal end
Escherichia coli
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
GTP + H2O
Escherichia coli
-
GDP + phosphate
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli
-
-
-
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
GTP + H2O
-
734245
Escherichia coli
GDP + phosphate
-
-
-
?
GTP + H2O
conserved bases in loop D specifically catalyze GTP hydrolysis, a guanine at residue 86 can compete with and substitute for G83 as a catalytic base, loop E controls the action of the distal end docking sites
734245
Escherichia coli
GDP + phosphate
-
-
-
?
Activating Compound (protein specific)
Activating Compound
Commentary
Organism
Structure
signal recognition particle RNA
SRP RNA, the signal recognition particle RNA distal end triggers GTP hydrolysis in the signal recognition particle protein-SRP receptor GTPase, i.e. Ffh-FtsY GTPase, complex. An intact docking site at the distal end of SRP RNA is required to stimulate GTPase activation. Loop E plays a crucial role in GTPase activation by the SRP RNA
Escherichia coli
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
C86A
mutations at C86 yield a more complex pattern: whereas C86A and C86U completely abolish GTPase activation by the RNA, C86 and C86G reduce GTPase activity by only 50%
Escherichia coli
C86G
mutations at C86 yield a more complex pattern: whereas C86A and C86U completely abolish GTPase activation by the RNA, DELTAC86 and C86G reduce GTPase activity by only 50%. Despite defective GTP hydrolysis, the G83A mutant shows any detectable defect in the efficiency of GTPase docking at the distal end
Escherichia coli
C86U
mutations at C86 yield a more complex pattern: whereas C86A and C86U completely abolish GTPase activation by the RNA, C86 and C86G reduce GTPase activity by only 50%
Escherichia coli
C87A/C97U
site-directed mutagenesis, combining C97U with C87A generates a superactive SRP RNA double mutant that hydrolyzes GTP 5.5fold faster than wild-type SRP RNA
Escherichia coli
C97U
site-directed mutagenesis, the mutant prolongs GTPase docking at the distal end, which correlates with its faster GTP hydrolysis rate
Escherichia coli
C97U/G99A
site-directed mutagenesis, combining G99A with C87A generate s a superactive SRP RNA double mutant that hydrolyzes GTP 4.6fold faster than wild-type SRP RNA
Escherichia coli
G83A
deletion or substitution of G83 by any other nucleotide completely abolishes the stimulatory effect of the SRP RNA on GTP hydrolysis. Despite defective GTP hydrolysis, the G83A mutant shows any detectable defect in the efficiency of GTPase docking at the distal end
Escherichia coli
G99A
site-directed mutagenesis, the mutant prolongs GTPase docking at the distal end, which correlates with its faster GTP hydrolysis rate
Escherichia coli
additional information
several mutants show higher GTPase activity than wild-type SRP RNA, most notably mutations at G99, U12, and C97. By modifying the GTPase docking interface, the efficiency of activation of the Ffh-FtsY GTPase complex can be specifically tuned. When G83 is mutated, substitution of C86 with guanine rescues the SRP RNA-mediated stimulation of GTPase activity to 50% of wild-type rate. Despite defective GTP hydrolysis, neither the G83A nor C86G mutant shows any detectable defect in the efficiency of GTPase docking at the distal end
Escherichia coli
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
GTP + H2O
Escherichia coli
-
GDP + phosphate
-
-
?
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
GTP + H2O
-
734245
Escherichia coli
GDP + phosphate
-
-
-
?
GTP + H2O
conserved bases in loop D specifically catalyze GTP hydrolysis, a guanine at residue 86 can compete with and substitute for G83 as a catalytic base, loop E controls the action of the distal end docking sites
734245
Escherichia coli
GDP + phosphate
-
-
-
?
General Information
General Information
Commentary
Organism
metabolism
in prokaryotic cells, the signal recognition particle consists of a SRP54 protein or Ffh and a 4.5S SRP RNA. Ffh contains a methionine-rich M domain, which binds the SRP RNA and the signal sequence on the translating ribosome. In addition, an NG domain in Ffh, comprising a GTPase G domain and a four-helix bundle N domain, forms a tight complex with a highly homologous NG domain in the SRP receptor, called FtsY in bacteria, in the presence of GTP. GTP hydrolysis at the end of the signal recognition particle cycle drives the disassembly of the Ffh-FtsY GTPase complex. The assembly of the signal recognition particle-FtsY GTPase complex and its GTPase activation require discrete conformational rearrangements in the signal recognition particle that are regulated by the RNC and the target membrane, respectively, thus ensuring the spatial and temporal precision of these molecular events during protein targeting, function of SRP RNA during co-translational protein targeting, overiew
Escherichia coli
additional information
bidentate interaction between the Ffh-FtsY GTPase complex and the distal end of the SRP RNA, overview. By modifying the GTPase docking interface, the efficiency of activation of the Ffh-FtsY GTPase complex can be specifically tuned. A guanine at residue 86 could compete with and substitute for G83 as a catalytic base. Conserved bases in loop D specifically catalyze GTP hydrolysis, a guanine at residue 86 can compete with and substitute for G83 as a catalytic base, loop E controls the action of the distal end docking sites
Escherichia coli
physiological function
the enzyme is involved in translocation of the signal recognition particle (SRP) RNA is a universally conserved and essential component of the SRP that mediates the co-translational targeting of proteins to the correct cellular membrane. During the targeting reaction, two functional ends in the signal recognition particle RNA mediate distinct functions. Whereas the RNA tetraloop facilitates initial assembly of two GTPases between the signal recognition particle and signal recognition particle receptor, this GTPase complex subsequently relocalizes about 100 A to the 5',3'-distal end of the RNA, a conformation crucial for GTPase activation and cargo handover
Escherichia coli
General Information (protein specific)
General Information
Commentary
Organism
metabolism
in prokaryotic cells, the signal recognition particle consists of a SRP54 protein or Ffh and a 4.5S SRP RNA. Ffh contains a methionine-rich M domain, which binds the SRP RNA and the signal sequence on the translating ribosome. In addition, an NG domain in Ffh, comprising a GTPase G domain and a four-helix bundle N domain, forms a tight complex with a highly homologous NG domain in the SRP receptor, called FtsY in bacteria, in the presence of GTP. GTP hydrolysis at the end of the signal recognition particle cycle drives the disassembly of the Ffh-FtsY GTPase complex. The assembly of the signal recognition particle-FtsY GTPase complex and its GTPase activation require discrete conformational rearrangements in the signal recognition particle that are regulated by the RNC and the target membrane, respectively, thus ensuring the spatial and temporal precision of these molecular events during protein targeting, function of SRP RNA during co-translational protein targeting, overiew
Escherichia coli
additional information
bidentate interaction between the Ffh-FtsY GTPase complex and the distal end of the SRP RNA, overview. By modifying the GTPase docking interface, the efficiency of activation of the Ffh-FtsY GTPase complex can be specifically tuned. A guanine at residue 86 could compete with and substitute for G83 as a catalytic base. Conserved bases in loop D specifically catalyze GTP hydrolysis, a guanine at residue 86 can compete with and substitute for G83 as a catalytic base, loop E controls the action of the distal end docking sites
Escherichia coli
physiological function
the enzyme is involved in translocation of the signal recognition particle (SRP) RNA is a universally conserved and essential component of the SRP that mediates the co-translational targeting of proteins to the correct cellular membrane. During the targeting reaction, two functional ends in the signal recognition particle RNA mediate distinct functions. Whereas the RNA tetraloop facilitates initial assembly of two GTPases between the signal recognition particle and signal recognition particle receptor, this GTPase complex subsequently relocalizes about 100 A to the 5',3'-distal end of the RNA, a conformation crucial for GTPase activation and cargo handover
Escherichia coli
Other publictions for EC 3.6.5.4
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [C]
Temperature Range [C]
Temperature Stability [C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [C] (protein specific)
Temperature Range [C] (protein specific)
Temperature Stability [C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
734245
Shen
Molecular mechanism of GTPase ...
Escherichia coli
J. Biol. Chem.
288
36385-36397
2013
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718911
Nguyen
Concerted complex assembly and ...
Arabidopsis thaliana
Biochemistry
50
7208-7217
2011
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721054
Ataide
The crystal structure of the s ...
Escherichia coli
Science
331
881-886
2011
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695328
Brooks
Structure of SRP14 from the Sc ...
Schizosaccharomyces pombe
Acta Crystallogr. Sect. D
65
421-433
2009
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698898
Marty
The membrane-binding motif of ...
Pisum sativum
J. Biol. Chem.
284
14891-14903
2009
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1
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701200
Buskiewicz
Conformation of the signal rec ...
Escherichia coli, Escherichia coli MRE 600
RNA
15
44-54
2009
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688395
Chandrasekar
Structure of the chloroplast s ...
Arabidopsis thaliana, Escherichia coli
J. Mol. Biol.
375
425-436
2008
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2
1
4
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696594
Abe
Pirh2 interacts with and ubiqu ...
Homo sapiens
Biomed. Res.
29
53-60
2008
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696602
Ananthamurthy
1H, 13C and 15N resonance assi ...
Arabidopsis thaliana
Biomol. NMR Assign.
2
37-39
2008
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698244
Rosch
The signal recognition particl ...
Streptococcus pyogenes, Streptococcus pyogenes HSC5
Infect. Immun.
76
2612-2619
2008
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699552
Kathir
Assembly of chloroplast signal ...
Arabidopsis thaliana
J. Mol. Biol.
381
49-60
2008
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700091
Dalley
Access to ribosomal protein Rp ...
Saccharomyces cerevisiae
Mol. Biol. Cell
19
2876-2884
2008
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700263
Maier
An amphiphilic region in the c ...
Escherichia coli, Escherichia coli MC1061
Mol. Microbiol.
68
1471-1484
2008
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700888
Egea
Structures of SRP54 and SRP19, ...
Pyrococcus furiosus
PLoS ONE
3
e3528
2008
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1
1
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4
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6
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700889
Egea
Structures of the signal recog ...
Pyrococcus furiosus
PLoS ONE
3
e3619
2008
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1
1
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7
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2
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4
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701197
van Nues
Roles for Srp72p in assembly, ...
Saccharomyces cerevisiae, Saccharomyces cerevisiae JDY819
RNA Biol.
5
73-83
2008
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701227
Stengel
Structural basis for specific ...
Arabidopsis thaliana
Science
321
253-256
2008
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2
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669133
Yurist
SRP19 is a dispensable compone ...
Haloferax volcanii
J. Bacteriol.
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276-279
2007
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686249
Bange
Protein translocation: checkpo ...
Escherichia coli, Thermus aquaticus
Curr. Biol.
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2007
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2
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686396
Gras
Structural insights into a new ...
Pyrococcus abyssi
EMBO Rep.
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569-575
2007
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1
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686752
Stengel
The structure of the chloropla ...
Arabidopsis thaliana
FEBS Lett.
581
5671-5676
2007
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687905
Shan
Conformational changes in the ...
Escherichia coli
J. Cell Biol.
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611-620
2007
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14
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688692
Gawronski-Salerno
Structure of the GMPPNP-stabil ...
Thermus aquaticus
J. Struct. Biol.
158
122-128
2007
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1
1
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688862
Salvetti
FlhF, a signal recognition par ...
Bacillus cereus
Microbiology
153
2541-2552
2007
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1
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1
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689926
Gawronski-Salerno
X-ray structure of the T. aqua ...
Thermus aquaticus
Proteins
66
984-995
2007
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1
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1
1
1
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1
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690025
Siu
SRP RNA provides the physiolog ...
Escherichia coli
RNA
13
240-250
2007
1
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1
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1
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3
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1
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7
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1
1
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7
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669525
Schlenker
The structure of the mammalian ...
Homo sapiens, Mus musculus
J. Biol. Chem.
281
8898-8906
2006
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2
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670045
Gariani
Conformational variability of ...
Mycoplasma mycoides
J. Struct. Biol.
153
85-96
2006
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670709
Fulton
The complete genome sequence o ...
Helicobacter pylori, Helicobacter pylori HPAG1
Proc. Natl. Acad. Sci. USA
103
9999-10004
2006
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6
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684117
Dong
Analysis of the GTPase activit ...
Streptomyces coelicolor
Acta Biochim. Biophys. Sin. (Shanghai)
38
467-476
2006
-
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1
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8
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10
3
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2
1
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3
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1
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1
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8
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1
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1
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1
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1
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-
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-
684156
Ramirez
Analysis of protein hydration ...
Thermus aquaticus
Acta Crystallogr. Sect. D
D62
1520-1534
2006
-
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1
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1
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687902
Angelini
Membrane binding of the bacter ...
Escherichia coli
J. Cell Biol.
174
715-724
2006
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1
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3
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1
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4
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1
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1
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1
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667665
Shan
Molecular crosstalk between th ...
Escherichia coli
Biochemistry
44
6214-6222
2005
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1
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668629
Shan
Co-translational protein targe ...
Thermus aquaticus
FEBS Lett.
579
921-926
2005
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1
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2
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669412
Sivaraja
Three-dimensional solution str ...
Arabidopsis thaliana
J. Biol. Chem.
280
41465-41471
2005
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1
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1
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669585
Lustig
The Trypanosoma brucei signal ...
Trypanosoma brucei
J. Cell Sci.
118
4551-4562
2005
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2
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1
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670368
Spanggord
RNA-mediated interaction betwe ...
Escherichia coli
Nat. Struct. Mol. Biol.
12
1116-1122
2005
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1
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-
-
-
-
-
-
-
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670873
Hainzl
Structural insights into SRP R ...
Methanocaldococcus jannaschii
RNA
11
1043-1050
2005
-
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-
1
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-
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2
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1
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659049
Zanen
FlhF, the third signal recogni ...
Bacillus subtilis, Bacillus subtilis 168
J. Bacteriol.
186
5956-5960
2004
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1
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-
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2
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1
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2
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2
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660000
Egea
Substrate twinning activates t ...
Thermus aquaticus
Nature
427
215-221
2004
1
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1
1
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1
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1
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1
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1
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1
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1
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1
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3
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668340
Schuenemann
Structure and function of the ...
Arabidopsis thaliana, Escherichia coli
Curr. Genet.
44
295-304
2004
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2
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5
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668656
Crowley
An ffh mutant of Streptococcus ...
Streptococcus mutans
FEMS Microbiol. Lett.
234
315-324
2004
-
-
-
-
-
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1
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669534
Dani
Advances in the structure and ...
Escherichia coli, Pyrococcus furiosus, Saccharomyces cerevisiae
J. Biol. Regul. Homeost. Agents
17
303-307
2004
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3
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-
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-
670366
Wild Klemen
SRP meets the ribosome ...
Escherichia coli, Saccharolobus solfataricus, Thermus aquaticus
Nat. Struct. Mol. Biol.
11
1049-1053
2004
-
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4
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3
-
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-
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-
670542
Rosenblad
Identification of chloroplast ...
Arabidopsis thaliana, Chlamydomonas sp., Chlorella vulgaris, Cyanidioschyzon merolae, Cyanidium caldarium, Epifagus virginiana, Guillardia theta, Mesostigma viride, Nephroselmis olivacea, Pisum sativum, Porphyra purpurea, Thalassiosira pseudonana, Trieres chinensis
Plant Cell Physiol.
45
1633-1639
2004
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23
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19
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23
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2
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-
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660347
Rosendal
Crystal structure of the compl ...
Saccharolobus solfataricus
Proc. Natl. Acad. Sci. USA
100
14701-14706
2003
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1
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1
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1
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2
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-
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-
660353
Shan
Induced nucleotide specificity ...
Escherichia coli
Proc. Natl. Acad. Sci. USA
100
4480-4485
2003
1
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1
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1
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Farmery
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