BRENDA - Enzyme Database show
show all sequences of 4.3.3.6

Crystal structure of Mycobacterium tuberculosis Rv2606c: a pyridoxal biosynthesis lyase

Kim, S.; Kim, K.J.; Biochem. Biophys. Res. Commun. 435, 255-259 (2013)

Data extracted from this reference:

Application
Application
Commentary
Organism
drug development
the enzyme is a target for anti-tuberculosis agents development
Mycobacterium tuberculosis
Cloned(Commentary)
Commentary
Organism
gene Rv2606c, recombinant expression of N-terminally His6-tagged enzyme with a TEV protease cleavage site in Escherichia coli strain B834
Mycobacterium tuberculosis
Crystallization (Commentary)
Crystallization
Organism
purified recombinant enzyme, hanging drop vapour diffusion method, mixing of 00.0015 ml of 22 mg/ml protein in 20 mM Tris-HCl, pH 8.0, and 5 mM 2-mercaptoethanol, with 0.0015 ml of reservoir solution, containing 8% PEG 8000, 0.1 M 3-[cyclohexylamino]-1-propanesulfonic acid, pH 10.5, and 0.2 M sodium chloride, and equilibration against 0.5 ml of reservoir solution, 20°C, X-ray diffraction structure determination and analysis at 1.8 A resolution, molecular replacement using the Thermotoga maritima PdxS, PDB code 2ISS
Mycobacterium tuberculosis
Engineering
Amino acid exchange
Commentary
Organism
H170N
site-directed mutagenesis
Mycobacterium tuberculosis
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
additional information
a glycerol molecule is bound at the active site of the enzyme structure through interactions with the conserved residues of Asp29 and Lys86
Mycobacterium tuberculosis
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Mycobacterium tuberculosis
P9WII9
gene Rv2606c
-
Mycobacterium tuberculosis H37Rv
P9WII9
gene Rv2606c
-
Purification (Commentary)
Commentary
Organism
recombinant N-terminally His6-tagged enzyme from Escherichia coli strain B834 by nickel affinity chromatography and cleavage of the tag by TEV protease, followed by anion exchange chromatography and gel filtration to about 95% purity
Mycobacterium tuberculosis
Subunits
Subunits
Commentary
Organism
More
from crystal structure, the asymmetric unit contains 3 Rv2606c molecules, and the dodecameric structure of the protein can be generated by applying crystallographic I222 symmetry, interfaces for the formation of dodecameric structure, overview
Mycobacterium tuberculosis
Application (protein specific)
Application
Commentary
Organism
drug development
the enzyme is a target for anti-tuberculosis agents development
Mycobacterium tuberculosis
Cloned(Commentary) (protein specific)
Commentary
Organism
gene Rv2606c, recombinant expression of N-terminally His6-tagged enzyme with a TEV protease cleavage site in Escherichia coli strain B834
Mycobacterium tuberculosis
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant enzyme, hanging drop vapour diffusion method, mixing of 00.0015 ml of 22 mg/ml protein in 20 mM Tris-HCl, pH 8.0, and 5 mM 2-mercaptoethanol, with 0.0015 ml of reservoir solution, containing 8% PEG 8000, 0.1 M 3-[cyclohexylamino]-1-propanesulfonic acid, pH 10.5, and 0.2 M sodium chloride, and equilibration against 0.5 ml of reservoir solution, 20°C, X-ray diffraction structure determination and analysis at 1.8 A resolution, molecular replacement using the Thermotoga maritima PdxS, PDB code 2ISS
Mycobacterium tuberculosis
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
H170N
site-directed mutagenesis
Mycobacterium tuberculosis
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
additional information
a glycerol molecule is bound at the active site of the enzyme structure through interactions with the conserved residues of Asp29 and Lys86
Mycobacterium tuberculosis
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant N-terminally His6-tagged enzyme from Escherichia coli strain B834 by nickel affinity chromatography and cleavage of the tag by TEV protease, followed by anion exchange chromatography and gel filtration to about 95% purity
Mycobacterium tuberculosis
Subunits (protein specific)
Subunits
Commentary
Organism
More
from crystal structure, the asymmetric unit contains 3 Rv2606c molecules, and the dodecameric structure of the protein can be generated by applying crystallographic I222 symmetry, interfaces for the formation of dodecameric structure, overview
Mycobacterium tuberculosis
General Information
General Information
Commentary
Organism
malfunction
the disruption of the PdxS gene generates a vitamin B6 auxotrophic Mycobacterium tuberculosis mutant
Mycobacterium tuberculosis
metabolism
the organism synthesizes pyridoxal 5'-phosphate via the deoxyxylulose 5-phosphate (DXP)-dependent pathway
Mycobacterium tuberculosis
additional information
the overall structure of the protein, composed of a (beta/alpha)8-barrel and two small 310-helices, is quite similar to those of other PdxS proteins. Rv2606c and Rv2604c form a stable complex, suggesting that these proteins might function as pyridoxal biosynthesis lyase and glutamine amidotransferase, respectively
Mycobacterium tuberculosis
physiological function
vitamin B6 biosynthesis is essential for the survival and virulence of Mycobacterium tuberculosis
Mycobacterium tuberculosis
General Information (protein specific)
General Information
Commentary
Organism
malfunction
the disruption of the PdxS gene generates a vitamin B6 auxotrophic Mycobacterium tuberculosis mutant
Mycobacterium tuberculosis
metabolism
the organism synthesizes pyridoxal 5'-phosphate via the deoxyxylulose 5-phosphate (DXP)-dependent pathway
Mycobacterium tuberculosis
additional information
the overall structure of the protein, composed of a (beta/alpha)8-barrel and two small 310-helices, is quite similar to those of other PdxS proteins. Rv2606c and Rv2604c form a stable complex, suggesting that these proteins might function as pyridoxal biosynthesis lyase and glutamine amidotransferase, respectively
Mycobacterium tuberculosis
physiological function
vitamin B6 biosynthesis is essential for the survival and virulence of Mycobacterium tuberculosis
Mycobacterium tuberculosis
Other publictions for EC 4.3.3.6
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)
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729134
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724219
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713758
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716306
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715491
Raschle
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J. Biol. Chem.
282
6098-6105
2007
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2
716736
Strohmeier
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103
19284-19289
2006
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715247
Burns
Reconstitution and biochemical ...
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J. Am. Chem. Soc.
127
3682-3683
2005
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715478
Raschle
On the two components of pyrid ...
Bacillus subtilis
J. Biol. Chem.
280
32291-32300
2005
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2