BRENDA - Enzyme Database
show all sequences of 7.6.2.8

Structural basis of nanobody-mediated blocking of BtuF, the cognate substrate-binding protein of the Escherichia coli vitamin B12 transporter BtuCD

Mireku, S.A.; Sauer, M.M.; Glockshuber, R.; Locher, K.P.; Sci. Rep. 7, 14296 (2017)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
recombinant expression of enzyme complex BtuCD-F in Escherichia coli strain BL21 (DE3) Gold
Escherichia coli
Crystallization (Commentary)
Crystallization
Organism
purified recombinant complex of inhibitory nanobody Nb9 with enzyme BtuF complex, crystallization solution contains 100 mM Tris-HCl, pH 8.5, 400 mM MgCl2, and 33% w/v PEG4000, X-ray diffraction structrue determination and analysis at 2.7 A resolution
Escherichia coli
Inhibitors
Inhibitors
Commentary
Organism
Structure
additional information
the vitamin B12 transporter of Escherichia coli, BtuCD-F is used as a model system by generating nanobodies against the periplasmic binding protein BtuF for transporter inhibition. Six isolated nanobodies are expressed in Escherichia coli strain WK-6, they compete with B12 for binding to BtuF with inhibition constants between 0.001 and 0.000001 mM. Structure analysis of BtuF in complex with the most effective nanobody Nb9 revealing the molecular basis of its inhibitory function, the nanobody binds to the cobalamin-binding pocket of BtuF, where BtuC-binding would occur, overview. Enzyme binding to immobilized recombinant His-tagged nanobodies. Competitive inhibition of cobalamin (Cbl) binding to BtuF by the selected nanobodies. Comparison of the Nb9-BtuF complex to Cbl-bound BtuF structures
Escherichia coli
Localization
Localization
Commentary
Organism
GeneOntology No.
Textmining
membrane
-
Escherichia coli
16020
-
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Mg2+
required
Escherichia coli
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ATP + H2O + vitamin B12-[cobalamin-binding protein][side 1]
Escherichia coli
-
ADP + phosphate + vitamin B12[side 2] + [cobalamin-binding protein][side 1]
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli
P06609 AND P06611 AND P37028
genes btuC, btuD, and btuF encoding for vitamin B12 import system permease protein BtuC, vitamin B12 import ATP-binding protein BtuD, and vitamin B12-binding protein BtuF
-
Purification (Commentary)
Commentary
Organism
preparation of spheroplasts of recombinnat enzyme in Escherichia coli strain BL21 (DE3) Gold membranes, recombinant enzyme and nanobody Nb9 in complex by BtuF pull-down affinity chromatography, and gel filtration
Escherichia coli
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ATP + H2O + vitamin B12-[cobalamin-binding protein][side 1]
-
752215
Escherichia coli
ADP + phosphate + vitamin B12[side 2] + [cobalamin-binding protein][side 1]
-
-
-
?
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
23
-
assay at
Escherichia coli
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Escherichia coli
Cofactor
Cofactor
Commentary
Organism
Structure
ATP
-
Escherichia coli
Ki Value [mM]
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
additional information
-
additional information
kinetics of binding and dissociation of nanobody-BtuF complexes, stopped-flow fluorescence kinetics, overview
Escherichia coli
Cloned(Commentary) (protein specific)
Commentary
Organism
recombinant expression of enzyme complex BtuCD-F in Escherichia coli strain BL21 (DE3) Gold
Escherichia coli
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
ATP
-
Escherichia coli
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant complex of inhibitory nanobody Nb9 with enzyme BtuF complex, crystallization solution contains 100 mM Tris-HCl, pH 8.5, 400 mM MgCl2, and 33% w/v PEG4000, X-ray diffraction structrue determination and analysis at 2.7 A resolution
Escherichia coli
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
additional information
the vitamin B12 transporter of Escherichia coli, BtuCD-F is used as a model system by generating nanobodies against the periplasmic binding protein BtuF for transporter inhibition. Six isolated nanobodies are expressed in Escherichia coli strain WK-6, they compete with B12 for binding to BtuF with inhibition constants between 0.001 and 0.000001 mM. Structure analysis of BtuF in complex with the most effective nanobody Nb9 revealing the molecular basis of its inhibitory function, the nanobody binds to the cobalamin-binding pocket of BtuF, where BtuC-binding would occur, overview. Enzyme binding to immobilized recombinant His-tagged nanobodies. Competitive inhibition of cobalamin (Cbl) binding to BtuF by the selected nanobodies. Comparison of the Nb9-BtuF complex to Cbl-bound BtuF structures
Escherichia coli
Ki Value [mM] (protein specific)
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
additional information
-
additional information
kinetics of binding and dissociation of nanobody-BtuF complexes, stopped-flow fluorescence kinetics, overview
Escherichia coli
Localization (protein specific)
Localization
Commentary
Organism
GeneOntology No.
Textmining
membrane
-
Escherichia coli
16020
-
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Mg2+
required
Escherichia coli
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ATP + H2O + vitamin B12-[cobalamin-binding protein][side 1]
Escherichia coli
-
ADP + phosphate + vitamin B12[side 2] + [cobalamin-binding protein][side 1]
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
preparation of spheroplasts of recombinnat enzyme in Escherichia coli strain BL21 (DE3) Gold membranes, recombinant enzyme and nanobody Nb9 in complex by BtuF pull-down affinity chromatography, and gel filtration
Escherichia coli
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ATP + H2O + vitamin B12-[cobalamin-binding protein][side 1]
-
752215
Escherichia coli
ADP + phosphate + vitamin B12[side 2] + [cobalamin-binding protein][side 1]
-
-
-
?
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
23
-
assay at
Escherichia coli
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Escherichia coli
General Information
General Information
Commentary
Organism
physiological function
bacterial ABC importers catalyze the uptake of essential nutrients including transition metals and metal-containing cofactors
Escherichia coli
General Information (protein specific)
General Information
Commentary
Organism
physiological function
bacterial ABC importers catalyze the uptake of essential nutrients including transition metals and metal-containing cofactors
Escherichia coli
Other publictions for EC 7.6.2.8
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)
749978
Agarwal
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Vibrio cholerae serotype O1, Vibrio cholerae serotype O1 ATCC 39541, Vibrio cholerae serotype O1 Classical Ogawa 395, Vibrio cholerae serotype O1 O395
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8
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1
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Okamoto
Characterization of human ATP ...
Homo sapiens
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496
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2
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750412
Santos
Functional and structural cha ...
Lactobacillus delbrueckii subsp. bulgaricus, Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842, Lactobacillus delbrueckii subsp. bulgaricus DSM 20081, Lactobacillus delbrueckii subsp. bulgaricus JCM 1002, Lactobacillus delbrueckii subsp. bulgaricus NBRC 13953, Lactobacillus delbrueckii subsp. bulgaricus NCIMB 11778
eLife
7
e35828
2018
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751644
Schmitt
Vitamin B12 import is all abo ...
Escherichia coli
Nat. Chem. Biol.
14
640-641
2018
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751670
Rempel
Cysteine-mediated decyanation ...
Thiobacillus denitrificans
Nat. Commun.
9
3038
2018
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751661
Goudsmits
Single-molecule visualization ...
Escherichia coli
Nat. Commun.
8
1652
2017
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752215
Mireku
Structural basis of nanobody- ...
Escherichia coli
Sci. Rep.
7
14296
2017
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752221
Mireku
Conformational change of a tr ...
Escherichia coli
Sci. Rep.
7
41575
2017
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3
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750063
Priess
Release of entropic spring re ...
Escherichia coli
Biophys. J.
110
2407-2418
2016
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751956
Pan
ATP hydrolysis induced confor ...
Escherichia coli
PLoS ONE
11
e0166980
2016
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752200
Kawaguchi
Translocation of the ABC tran ...
Homo sapiens
Sci. Rep.
6
30183
2016
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734003
Su
Conformational motions and fun ...
Escherichia coli
Int. J. Mol. Sci.
16
17933-17951
2015
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Conformational cycle of the vi ...
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Structure of AMP-PNP-bound Btu ...
Escherichia coli
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21
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734820
Gopinath
A vitamin B12 transporter in M ...
Mycobacterium tuberculosis
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3
120175
2013
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720849
Weng
-
The conformational transition ...
Escherichia coli
PLoS ONE
7
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2012
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734771
Korkhov
Structure of AMP-PNP-bound vit ...
Escherichia coli
Nature
490
367-372
2012
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719930
Di Bartolo
In vitro folding and assembly ...
Escherichia coli
J. Biol. Chem.
286
18807-18815
2011
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