BRENDA - Enzyme Database
show all sequences of 7.6.2.8

Cysteine-mediated decyanation of vitamin B12 by the predicted membrane transporter BtuM

Rempel, S.; Colucci, E.; de Gier, J.W.; Guskov, A.; Slotboom, D.J.; Nat. Commun. 9, 3038 (2018)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
gene Tbd_2719 or btuM, recombinant expression of codon-optimized enzyme in Escherichia coli strain MC1061 and in Escherichia coli strain JW0154 (DELTAbtuF::KmR::DELTA FEC) lacking active BtuF and BtuC, overexpression of His-tagged enzyme and of EPEA-tagged enzyme
Thiobacillus denitrificans
Crystallization (Commentary)
Crystallization
Organism
purified recombinant His-tagged enzyme BtuM with natively bound cobalmin and anomalously bound cobalmin, sitting drop vapour diffusion method, mixing of 0.002 ml of protein in 50mM Tris-HCl, pH 7.5, or in 50 mM HEPES-NaOH pH 8.0, 100 mM NaCl, 0.005 mM cyano-Cbl and 0.35% detergent, with 0.002 ml of precipitant solution containing 25 mM Tris, pH 8.5, and 25-30% v/v PEG 400 or 50 mM Tris, pH 8.5, and 27-30% v/v PEG 400, or 75 mM Tris, pH 8.5, and 29-30% v/v PEG 400, at 8°C, 3-4 weeks, X-ray diffraction structure determination and analysis at 2.0-2.5 A resolution, structure modeling
Thiobacillus denitrificans
Localization
Localization
Commentary
Organism
GeneOntology No.
Textmining
inner membrane
integral membrane enzyme
Thiobacillus denitrificans
-
-
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Mg2+
required
Thiobacillus denitrificans
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]
Thiobacillus denitrificans
-
ADP + phosphate + vitamin B12[side 2] + [cobalamin-binding protein][side 1]
-
-
?
additional information
Thiobacillus denitrificans
BtuM binds vitamin B12 in its base-off conformation, in which the 5,6-dimethylbenzimidazole moiety does not bind to the cobalt ion, but with a cysteine residue as axial ligand of the corrin cobalt ion, BtuMTd binds cobalamin (Cbl) using cysteine ligation. In contrast, at physiological pH the conformation of free Cbl in aqueous solution is base-on with the 5,6-dimethylbenzimidazole moiety coordinated to the cobalt ion in the alpha-axial position
?
-
-
-
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Thiobacillus denitrificans
Q3SFD8
-
-
Purification (Commentary)
Commentary
Organism
recombinant His-tagged enzyme to homogeneity by nickel affnity chromatography in presence of 0.35% n-nonyl-beta-D-glucopyranoside, gel filtration, and ultrafiltration, recombinant EPEA-tagged enzyme by affinity chromatography and ultrafiltration
Thiobacillus denitrificans
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ATP + H2O + cobinamide-[cobalamin-binding protein][side 1]
-
751670
Thiobacillus denitrificans
ADP + phosphate + cobinamide[side 2] + [cobalamin-binding protein][side 1]
-
-
-
?
ATP + H2O + vitamin B12-[cobalamin-binding protein][side 1]
-
751670
Thiobacillus denitrificans
ADP + phosphate + vitamin B12[side 2] + [cobalamin-binding protein][side 1]
-
-
-
?
additional information
BtuM binds vitamin B12 in its base-off conformation, in which the 5,6-dimethylbenzimidazole moiety does not bind to the cobalt ion, but with a cysteine residue as axial ligand of the corrin cobalt ion, BtuMTd binds cobalamin (Cbl) using cysteine ligation. In contrast, at physiological pH the conformation of free Cbl in aqueous solution is base-on with the 5,6-dimethylbenzimidazole moiety coordinated to the cobalt ion in the alpha-axial position
751670
Thiobacillus denitrificans
?
-
-
-
-
additional information
BtuM binds vitamin B12 in its base-off conformation, in which the 5,6-dimethylbenzimidazole moiety does not bind to the cobalt ion, but with a cysteine residue as axial ligand of the corrin cobalt ion, BtuMTd binds cobalamin (Cbl) using cysteine ligation. In contrast, at physiological pH the conformation of free Cbl in aqueous solution is base-on with the 5,6-dimethylbenzimidazole moiety coordinated to the cobalt ion in the alpha-axial position. The membrane environment also appears to preclude Cbl binding to purified BtuMTd, as binding is observed only when the substrate is added before solubilisation. BtuMTd also catalyses cysteine-mediated decyanation of vitamin B12
751670
Thiobacillus denitrificans
?
-
-
-
-
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
22
-
assay at room temperature
Thiobacillus denitrificans
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Thiobacillus denitrificans
Cofactor
Cofactor
Commentary
Organism
Structure
ATP
-
Thiobacillus denitrificans
Cloned(Commentary) (protein specific)
Commentary
Organism
gene Tbd_2719 or btuM, recombinant expression of codon-optimized enzyme in Escherichia coli strain MC1061 and in Escherichia coli strain JW0154 (DELTAbtuF::KmR::DELTA FEC) lacking active BtuF and BtuC, overexpression of His-tagged enzyme and of EPEA-tagged enzyme
Thiobacillus denitrificans
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
ATP
-
Thiobacillus denitrificans
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant His-tagged enzyme BtuM with natively bound cobalmin and anomalously bound cobalmin, sitting drop vapour diffusion method, mixing of 0.002 ml of protein in 50mM Tris-HCl, pH 7.5, or in 50 mM HEPES-NaOH pH 8.0, 100 mM NaCl, 0.005 mM cyano-Cbl and 0.35% detergent, with 0.002 ml of precipitant solution containing 25 mM Tris, pH 8.5, and 25-30% v/v PEG 400 or 50 mM Tris, pH 8.5, and 27-30% v/v PEG 400, or 75 mM Tris, pH 8.5, and 29-30% v/v PEG 400, at 8°C, 3-4 weeks, X-ray diffraction structure determination and analysis at 2.0-2.5 A resolution, structure modeling
Thiobacillus denitrificans
Localization (protein specific)
Localization
Commentary
Organism
GeneOntology No.
Textmining
inner membrane
integral membrane enzyme
Thiobacillus denitrificans
-
-
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Mg2+
required
Thiobacillus denitrificans
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]
Thiobacillus denitrificans
-
ADP + phosphate + vitamin B12[side 2] + [cobalamin-binding protein][side 1]
-
-
?
additional information
Thiobacillus denitrificans
BtuM binds vitamin B12 in its base-off conformation, in which the 5,6-dimethylbenzimidazole moiety does not bind to the cobalt ion, but with a cysteine residue as axial ligand of the corrin cobalt ion, BtuMTd binds cobalamin (Cbl) using cysteine ligation. In contrast, at physiological pH the conformation of free Cbl in aqueous solution is base-on with the 5,6-dimethylbenzimidazole moiety coordinated to the cobalt ion in the alpha-axial position
?
-
-
-
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant His-tagged enzyme to homogeneity by nickel affnity chromatography in presence of 0.35% n-nonyl-beta-D-glucopyranoside, gel filtration, and ultrafiltration, recombinant EPEA-tagged enzyme by affinity chromatography and ultrafiltration
Thiobacillus denitrificans
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ATP + H2O + cobinamide-[cobalamin-binding protein][side 1]
-
751670
Thiobacillus denitrificans
ADP + phosphate + cobinamide[side 2] + [cobalamin-binding protein][side 1]
-
-
-
?
ATP + H2O + vitamin B12-[cobalamin-binding protein][side 1]
-
751670
Thiobacillus denitrificans
ADP + phosphate + vitamin B12[side 2] + [cobalamin-binding protein][side 1]
-
-
-
?
additional information
BtuM binds vitamin B12 in its base-off conformation, in which the 5,6-dimethylbenzimidazole moiety does not bind to the cobalt ion, but with a cysteine residue as axial ligand of the corrin cobalt ion, BtuMTd binds cobalamin (Cbl) using cysteine ligation. In contrast, at physiological pH the conformation of free Cbl in aqueous solution is base-on with the 5,6-dimethylbenzimidazole moiety coordinated to the cobalt ion in the alpha-axial position
751670
Thiobacillus denitrificans
?
-
-
-
-
additional information
BtuM binds vitamin B12 in its base-off conformation, in which the 5,6-dimethylbenzimidazole moiety does not bind to the cobalt ion, but with a cysteine residue as axial ligand of the corrin cobalt ion, BtuMTd binds cobalamin (Cbl) using cysteine ligation. In contrast, at physiological pH the conformation of free Cbl in aqueous solution is base-on with the 5,6-dimethylbenzimidazole moiety coordinated to the cobalt ion in the alpha-axial position. The membrane environment also appears to preclude Cbl binding to purified BtuMTd, as binding is observed only when the substrate is added before solubilisation. BtuMTd also catalyses cysteine-mediated decyanation of vitamin B12
751670
Thiobacillus denitrificans
?
-
-
-
-
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
22
-
assay at room temperature
Thiobacillus denitrificans
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Thiobacillus denitrificans
General Information
General Information
Commentary
Organism
evolution
the enzyme is a ABC transporter, all ABC-type ATPases encoded by the organism are predicted to be part of classical ABC transporters, and not ECF transporters. The organism does not encode an ECF-module. BtuM homologues (apart from one exception) are found exclusively in organisms lacking an ECF-module. But BtuMTd structurally resembles the S-components of ECF transporters
Thiobacillus denitrificans
additional information
function and structure of BtuMTd, cobalamin binding structure, overview
Thiobacillus denitrificans
physiological function
the membrane protein BtuM acts as transporter for uptake of essential vitamin B12, i.e. cobalamin, one of the most complex cofactors known, and used by enzymes catalyzing for instance methyl-group transfer and ribonucleotide reduction reactions. BtuMTd likely combines two functions: transport of the substrate into the bacterial cell, and chemical modification of the substrate. A cobalt-cysteine interaction allows for chemical modification of the substrate prior to translocation, which is a rare feature among uptake systems. BtuM homologues are small membrane proteins of about 22 kDa, and found predominantly in Gram-negative species, distributed mostly over alpha-, beta-, and gamma-proteobacteria
Thiobacillus denitrificans
General Information (protein specific)
General Information
Commentary
Organism
evolution
the enzyme is a ABC transporter, all ABC-type ATPases encoded by the organism are predicted to be part of classical ABC transporters, and not ECF transporters. The organism does not encode an ECF-module. BtuM homologues (apart from one exception) are found exclusively in organisms lacking an ECF-module. But BtuMTd structurally resembles the S-components of ECF transporters
Thiobacillus denitrificans
additional information
function and structure of BtuMTd, cobalamin binding structure, overview
Thiobacillus denitrificans
physiological function
the membrane protein BtuM acts as transporter for uptake of essential vitamin B12, i.e. cobalamin, one of the most complex cofactors known, and used by enzymes catalyzing for instance methyl-group transfer and ribonucleotide reduction reactions. BtuMTd likely combines two functions: transport of the substrate into the bacterial cell, and chemical modification of the substrate. A cobalt-cysteine interaction allows for chemical modification of the substrate prior to translocation, which is a rare feature among uptake systems. BtuM homologues are small membrane proteins of about 22 kDa, and found predominantly in Gram-negative species, distributed mostly over alpha-, beta-, and gamma-proteobacteria
Thiobacillus denitrificans
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
Mechanistic basis of vitamin ...
Vibrio cholerae serotype O1, Vibrio cholerae serotype O1 ATCC 39541, Vibrio cholerae serotype O1 Classical Ogawa 395, Vibrio cholerae serotype O1 O395
Biochim. Biophys. Acta
1867
140-151
2019
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20
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1
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749821
Okamoto
Characterization of human ATP ...
Homo sapiens
Biochem. Biophys. Res. Commun.
496
1122-1127
2018
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2
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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1
1
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6
1
1
1
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12
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8
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18
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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6
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1
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12
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18
1
1
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1
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2
2
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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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1
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2
2
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751670
Rempel
Cysteine-mediated decyanation ...
Thiobacillus denitrificans
Nat. Commun.
9
3038
2018
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1
1
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1
1
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2
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1
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1
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4
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1
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4
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1
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1
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3
3
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751661
Goudsmits
Single-molecule visualization ...
Escherichia coli
Nat. Commun.
8
1652
2017
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1
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5
1
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1
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3
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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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1
8
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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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734281
Joseph
Conformational cycle of the vi ...
Escherichia coli
J. Biol. Chem.
289
3176-3185
2014
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734760
Korkhov
Structure of AMP-PNP-bound Btu ...
Escherichia coli
Nat. Struct. Mol. Biol.
21
1097-1099
2014
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