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propane-1,2-diol = propanal + H2O
propane-1,2-diol = propanal + H2O
binding of the substrate to the active site converts a hexacoordinated complex of K+ into the heptacoordinated one. A relatively large binding energy is released upon coordination of the two hydroxyl groups to K+, displacing a sixth ligand, H2O. Interaction of the coenzyme with the enzyme cleaves its Co-C bond, forming an adenosyl radical and cob(II)alamin. The radical abstracts the pro-S hydrogen of the S-enantiomer forming a substrate-derived radical and 5'-deoxyadenosine. The substrate-radical undergoes the 1,2-shift of the hydroxyl group, forming a product-derived gem-diol radical. The C2 of the product radical, abstracts a hydrogen back from deoxyadenosine with inversion of the configuration of C2, producing a 1,1-gem-diol, which undergoes dehydration, forming propionaldehyde and H2O
-
propane-1,2-diol = propanal + H2O
enzymatic radical catalysis, with adenosylcobalamin, coenzyme B12, as a cofactor. Dehydration of 1,2-diols to the corresponding aldehydes. The substrate and an essential potassium ion are located inside a betaalpha8 barrel. Two hydroxyl groups of the substrate coordinate directly to the potassium ion which binds to the negatively charged inner part of the cavity. Cobalamin bound covers the cavity to isolate the active site from the solvent. The initial migration of the hydroxyl group is stereospecific and the dehydration of a gem-diol undergoes steric control by the enzyme
-
propane-1,2-diol = propanal + H2O
the enzyme-bound adenosylcobalamin serves as an intermediate hydrogen carrier, accepting a hydrogen atom from C1 of the substrate to C5' of the coenzyme and giving a hydrogen back to C2 of the product. R and S enantiomers are bound to the active site of the enzyme in a symmetrical mode with respect to the plane
-
propane-1,2-diol = propanal + H2O
minimal mechanism for AdoCbl-dependent diol dehydratase involving the cob(II)alamin cofactor and active-site structure of the enzyme, overview
-
propane-1,2-diol = propanal + H2O
reaction mechanism, quantum mechanical/molecular mechanical, QM/MM, modeling of diol dehydratase based on the crystal structure of diol dehydratase-adeninylpentylcobalamin complex, overview. The hydrogen recombination is the rate-determining step for the overall reaction
-
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cyanocobalamin
a tightly bound inactive coenzyme analogue lacking the adenine ring in the upper axial ligand, imitates the inactivated cofactor
3-butene-1,2-diol
-
holodiol dehydratase undergoes rapid and irreversible inactivation, the inactivation cleaves the Co-C bond of adenosylcobalamin irreversibly forming unidentified radicals and cob(II)alamin that resist oxidation even in the presence of oxygen, inactivation mechanism, overview
3-butyne-1,2-diol
-
holodiol dehydratase undergoes rapid and irreversible inactivation, the inactivation cleaves the Co-C bond of adenosylcobalamin irreversibly forming unidentified radicals and cob(II)alamin that resist oxidation even in the presence of oxygen, inactivation mechanism, overview
adenosylcobinamide 3-(2-methylbenzimidazolyl)propyl phosphate
-
competitive inhibitor with respect to coenzyme B12. Irreversible cleavage of the coenzyme Co-C bond during the inactivation
-
adenosylethylcobalamin
-
strong competitive inhibitor
adenosylpentylcobalamin
-
strong competitive inhibitor
cyanocobalamin
a tightly bound inactive coenzyme analogue lacking the adenine ring in the upper axial ligand, imitates the inactivated cofactor
EDTA
-
EDTA inhibition of apoenzyme is reversible at least in the initial phase
O2
-
irreversible inactivation
thioglycerol
-
holodiol dehydratase undergoes rapid and irreversible inactivation, the inactivation cleaves the Co-C bond of adenosylcobalamin irreversibly forming unidentified radicals and cob(II)alamin that resist oxidation even in the presence of oxygen, inactivation mechanism, overview
glycerol
-
glycerol
adenosylcobalamin-dependent diol dehydratase undergoes suicide inactivation by glycerol, one of its physiological substrates, resulting in the irreversible cleavage of the coenzyme Co-C bond. The damaged cofactor remains tightly bound to the active site, it is not displaced by intact adenosylcobalamin, resulting in the irreversible inactivation of the enzyme. The DD-reactivating factor reactivates the inactivated holoenzyme in the presence of ATP and Mg2+ by mediating the exchange of the tightly bound damaged cofactor for free intact coenzyme, overview
adenosylmethylcobalamin
-
-
adenosylmethylcobalamin
-
catalytic efficiency (turnover number to Km-value) of the holoenzyme with adenosylmethylcobalamin is 0.15% of that for the regular coenzyme adenosylcobalamin, Km: 0.0017 mM
glycerol
-
reaction ceases within several min
glycerol
adenosylcobalamin-dependent diol dehydratase undergoes suicide inactivation by glycerol, one of its physiological substrates, resulting in the irreversible cleavage of the coenzyme Co-C bond. The damaged cofactor remains tightly bound to the active site, it is not displaced by intact adenosylcobalmin, resulting in the irreversible inactivation of the enzyme. The DD-reactivating factor reactivates the inactivated holoenzyme in the presence of ATP and Mg2+ by mediating the exchange of the tightly bound damaged cofactor for free intact coenzyme, overview
glycerol
adenosylcobalamin-dependent diol dehydratase undergoes suicide inactivation by glycerol, one of its physiological substrates, resulting in the irreversible cleavage of the coenzyme Co-C bond. The damaged cofactor remains tightly bound to the active site, it is not displaced by intact Ado-Cbl, resulting in the irreversible inactivation of the enzyme. The DD-reactivating factor reactivates the inactivated holoenzyme in the presence of ATP and Mg2+ by mediating the exchange of the tightly bound damaged cofactor for free intact coenzyme, overview
Propane-1,2-diol
-
leads to inactivation of wild-type and mutant enzymes during catalysis, kinetics, overview
Propane-1,2-diol
-
mechanism-based inactivation obeying first-order reaction kinetics
additional information
-
inactivated holoenzymes undergo reactivation by diol dehydratase-reactivating factor in the presence of ATP, Mg2+ and adenosylcobalamin
-
additional information
-
Asp335 has a strong anticatalytic effect on the OH group migration despite its important role in substrate binding. The synergistic interplay of the O-C bond cleavage by Ca2+ ion and the deprotonation of the spectator OH-group by Glu170 is required to overcome the anticatalytic effect of Asp335
-
additional information
-
no inhibition by 5 mM of 1,10-phenanthroline, 2,2'-dipyridyl, citrate, succinate, tartrate, malate, and salicylate
-
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0.47 - 3.9
(R)-Propane-1,2-diol
0.11 - 2.6
(S)-propane-1,2-diol
0.031 - 1.9
Propane-1,2-diol
2.5
1,2-Butanediol
-
pH 8.0, 37°C
0.04 - 10
1,2-propanediol
0.00082 - 0.0027
adenosylcobinamide 3-benzimidazolylpropyl phosphate
0.00099
adenosylcobinamide 3-imidazolylpropyl phosphate
-
-
0.00029
adenosylcobinamide 3-pyridylpropyl phosphate
-
-
0.00096
cobeta-adenosyl-coalpha-benzimidazolylcobamide
-
-
0.00104
cobeta-adenosyl-coalpha-imidazolylcobamide
-
-
0.12 - 1.9
Propan-1,2-diol
0.22 - 0.3
Propane-1,2-diol
additional information
additional information
-
0.47
(R)-Propane-1,2-diol
wild type enzyme, at pH 8.0 and 37°C
0.7
(R)-Propane-1,2-diol
mutant enzyme S301A, at pH 8.0 and 37°C
2.1
(R)-Propane-1,2-diol
mutant enzyme Q336A, at pH 8.0 and 37°C
3.9
(R)-Propane-1,2-diol
mutant enzyme S301A/Q336A, at pH 8.0 and 37°C
0.11
(S)-propane-1,2-diol
wild type enzyme, at pH 8.0 and 37°C
0.26
(S)-propane-1,2-diol
mutant enzyme S301A, at pH 8.0 and 37°C
0.66
(S)-propane-1,2-diol
mutant enzyme Q336A, at pH 8.0 and 37°C
2.6
(S)-propane-1,2-diol
mutant enzyme S301A/Q336A, at pH 8.0 and 37°C
0.031
Propane-1,2-diol
mutant T172A, pH not specified in the publication, temperature not specified in the publication
0.15
Propane-1,2-diol
wild-type, pH not specified in the publication, temperature not specified in the publication
0.15
Propane-1,2-diol
mutant S224A, pH not specified in the publication, temperature not specified in the publication
0.16
Propane-1,2-diol
mutant T172S, pH not specified in the publication, temperature not specified in the publication
0.51
Propane-1,2-diol
mutant S224C, pH not specified in the publication, temperature not specified in the publication
1.9
Propane-1,2-diol
mutant S224N, pH not specified in the publication, temperature not specified in the publication
0.04
1,2-propanediol
-
-
0.08
1,2-propanediol
-
pH 8.0, 37°C
0.08
1,2-propanediol
-
mutant S362A
0.1
1,2-propanediol
-
mutant Q141A
10
1,2-propanediol
-
mutant Q296A
0.00082
adenosylcobinamide 3-benzimidazolylpropyl phosphate
-
-
0.0027
adenosylcobinamide 3-benzimidazolylpropyl phosphate
-
-
0.26
Cobalamin
-
pH 8.0, 37°C, mutant Halpha143Q
0.9
Cobalamin
-
pH 8.0, 37°C, wild-type enzyme
0.12
Propan-1,2-diol
-
pH 8.0, 37°C, mutant Kbeta135R
0.15
Propan-1,2-diol
-
pH 8.0, 37°C, wild-type enzyme and mutant Salpha224A
0.39
Propan-1,2-diol
-
pH 8.0, 37°C, mutant Kbeta135A and mutant Kbeta135Q
0.4
Propan-1,2-diol
-
pH 8.0, 37°C, mutant Kbeta135E
1.9
Propan-1,2-diol
-
pH 8.0, 37°C, mutant Salpha224N
0.22
Propane-1,2-diol
-
pH 8.0, 37°C, wild-type enzyme
0.3
Propane-1,2-diol
-
pH 8.0, 37°C, mutant Halpha143Q
additional information
additional information
-
kinetic analysis of mutant enzymes, overview
-
additional information
additional information
-
kinetic analysis with substrate analogues 3-butene-1,2-diol, 3-butyne-1,2-diol or thioglycerol
-
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0.5 - 336
Propane-1,2-diol
7.8
1,2-Butanediol
-
pH 8.0, 37°C
366
1,2-propanediol
-
pH 8.0, 37°C
0.03 - 354
Propane-1,2-diol
0.5
Propane-1,2-diol
mutant T172A, pH not specified in the publication, temperature not specified in the publication
12
Propane-1,2-diol
mutant S224C, pH not specified in the publication, temperature not specified in the publication
17
Propane-1,2-diol
mutant S224N, pH not specified in the publication, temperature not specified in the publication
34
Propane-1,2-diol
mutant T172S, pH not specified in the publication, temperature not specified in the publication
64
Propane-1,2-diol
mutant S224A, pH not specified in the publication, temperature not specified in the publication
336
Propane-1,2-diol
wild-type, pH not specified in the publication, temperature not specified in the publication
7.7
CN-cobalamin
-
pH 8.0, 37°C, mutant Kbeta135E
17
CN-cobalamin
-
pH 8.0, 37°C, mutant Salpha224A
64
CN-cobalamin
-
pH 8.0, 37°C, mutant Kbeta135R
196
CN-cobalamin
-
pH 8.0, 37°C, mutant Kbeta135A
211
CN-cobalamin
-
pH 8.0, 37°C, mutant Kbeta135Q
254
CN-cobalamin
-
pH 8.0, 37°C, mutant Salpha224N
336
CN-cobalamin
-
pH 8.0, 37°C, wild-type enzyme
0.03
Propane-1,2-diol
-
pH 8.0, 37°C, mutant Halpha143L
5.1
Propane-1,2-diol
-
pH 8.0, 37°C, mutant Halpha143A
121
Propane-1,2-diol
-
pH 8.0, 37°C, mutant Halpha143Q
354
Propane-1,2-diol
-
pH 8.0, 37°C, wild-type enzyme
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D335A
computational mutation study. The OH group migration is accelerated in the Asp335Ala mutant, due to the absence of the electric repulsion between Asp335 and the migrating OH group
E170A E170Q
computational mutation study. The spectator OH group is not fully activated in the Glu170Gln and Glu170Ala mutants during the OH group migration, and thus the activation energies in the Glu170Gln and Glu170Ala mutants are higher than that in the wild-type enzyme
E170Q
computational mutation study. The spectator OH group is not fully activated in the Glu170Gln and Glu170Ala mutants during the OH group migration, and thus the activation energies in the Glu170Gln and Glu170Ala mutants are higher than that in the wild-type enzyme
H143A
computational mutation study. The resonance stabilization of the transition state in the OH group migration is observed in the wild-type enzyme while not in the His143Ala mutant. Since the cleavage of the C2-oxygen bond of 1,2-diol radical proceeds in a more homolytic manner in the His143Ala mutant, Glu170 cannot effectively deprotonate the spectator OH group in the transition state, leading to increased activation energy of the OH group migration in the His143Ala mutant
Q336A
the mutant shows decreased activity (21%) compared to the wild type enzyme
S224A
mutation in alpha-subunit, a key residue for stabilizing the post-homolysis state of the adenosyl group. More than 5fold reduction in kcat/Km
S224C
mutation in alpha-subunit, a key residue for stabilizing the post-homolysis state of the adenosyl group. About 100fold reduction in kcat/Km
S224N
mutation in alpha-subunit, a key residue for stabilizing the post-homolysis state of the adenosyl group. More than 100fold reduction in kcat/Km
S301A
the mutant shows decreased activity (76%) compared to the wild type enzyme
S301A/Q336A
the mutant shows lowest activity (9.8%) compared to the wild type enzyme
T172A
mutation in alpha-subunit, a key residue for stabilizing the post-homolysis state of the adenosyl group. More than 100fold reduction in kcat/Km
T172S
mutation in alpha-subunit, a key residue for stabilizing the post-homolysis state of the adenosyl group. More than 10fold reduction in kcat/Km
E170H
-
does not form (alpha-beta-gamma)complex
E221A
-
does not form (alpha-beta-gamma)complex
H143A
-
only very little activity
Halpha143A
-
site-directed mutagenesis, the mutant shows residual activity compared to the wild-type enzyme
Halpha143E
-
site-directed mutagenesis, the mutant is inactive and does not form (alphabeta)2 complexes
Halpha143K
-
site-directed mutagenesis, the mutant is inactive and does not form (alphabeta)2 complexes
Halpha143L
-
site-directed mutagenesis, the mutant shows residual activity compared to the wild-type enzyme
Halpha143Q
-
site-directed mutagenesis, the mutant shows residual activity compared to the wild-type enzyme, irreversible inactivation by O2 in the absence of substrate at a much lower rate than the wild type, preference of the Halpha143Q mutant for (R)- and (S)-1,2-propanediols, kinetic parameters for each enantiomer, overview
Kbeta135A
-
site-directed mutagenesis, the mutant shows 42% reduced activity compared to the wild-type enzyme, the mutant is less sensitive to inhibitor CN-cobalamin
Kbeta135E
-
site-directed mutagenesis, the mutant shows 98% reduced activity compared to the wild-type enzyme
Kbeta135Q
-
site-directed mutagenesis, the mutant shows 27% reduced activity compared to the wild-type enzyme, the mutant is less sensitive to inhibitor CN-cobalamin
Kbeta135R
-
site-directed mutagenesis, the mutant shows 24% reduced activity compared to the wild-type enzyme
Q296A
-
increased Km for substrate(1,2-propanediol) by a factor of 250
Salpha224A
-
site-directed mutagenesis, the mutant shows 81% reduced activity compared to the wild-type enzyme, mechanism-based complete inactivation of the Salpha224A holoenzyme during catalysis by propan-1,2-diol leading to accumulation of cobalamin, mechanism, overview
Salpha224N
-
site-directed mutagenesis, the mutant shows 95% reduced activity compared to the wild-type enzyme
additional information
-
construction of chimeric enzymes with subunit compositions alphaGbetaD2GgammaG and alphaGbetaGgammaDG, overview
D335A
-
inactive mutant
D335A
-
does not form (alpha-beta-gamma)complex
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Tobimatsu, T.; Kajiura, H.; Toraya, T.
Specificities of reactivating factors for adenosylcobalamin-dependent diol dehydratase and glycerol dehydratase
Arch. Microbiol.
174
81-88
2000
Klebsiella oxytoca, Klebsiella pneumoniae
brenda
Mori, K.; Toraya, T.
Mechanism of reactivation of coenzyme B12-dependent diol dehydratase by a molecular chaperone-like reactivating factor
Biochemistry
38
13170-13178
1999
Klebsiella oxytoca
brenda
Toraya, T.
Radical catalysis of B12 enzymes: structure, mechanism, inactivation, and reactivation of diol and glycerol dehydratases
Cell. Mol. Life Sci.
57
106-127
2000
Klebsiella oxytoca, Klebsiella pneumoniae
brenda
Fukuoka, M.; Yamada, S.; Miyoshi, S.; Yamashita, K.; Yamanishi, M.; Zou, X.; Brown, K.L.; Toraya, T.
Functions of the D-ribosyl moiety and the lower axial ligand of the nucleotide loop of coenzyme B(12) in diol dehydratase and ethanolamine ammonia-lyase reactions
J. Biochem.
132
935-943
2002
Klebsiella oxytoca
brenda
Shibata, N.; Nakanishi, Y.; Fukuoka, M.; Yamanishi, M.; Yasuoka, N.; Toraya, T.
Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase
J. Biol. Chem.
278
22717-22725
2003
Klebsiella oxytoca
brenda
Masuda, J.; Shibata, N.; Morimoto, Y.; Toraya, T.; Yasuoka, N.
How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex
Structure Fold. Des.
8
775-788
2000
Klebsiella oxytoca
brenda
Fukuoka, M.; Nakanishi, Y.; Hannak, R.B.; Krautler, B.; Toraya, T.
Homoadenosylcobalamins as probes for exploring the active sites of coenzyme B12-dependent diol dehydratase and ethanolamine ammonia-lyase
FEBS J.
272
4787-4796
2005
Klebsiella oxytoca
brenda
Tobimatsu, T.; Kawata, M.; Toraya, T.
The N-terminal regions of beta and gamma subunits lower the solubility of adenosylcobalamin-dependent diol dehydratase
Biosci. Biotechnol. Biochem.
69
455-462
2005
Klebsiella oxytoca
brenda
Kajiura, H.; Mori, K.; Shibata, N.; Toraya, T.
Molecular basis for specificities of reactivating factors for adenosylcobalamin-dependent diol and glycerol dehydratases
FEBS J.
274
5556-5566
2007
Klebsiella oxytoca, Klebsiella pneumoniae
brenda
Sakai, T.; Yamasaki, A.; Toyofuku, S.; Nishiki, T.; Yunoki, M.; Komoto, N.; Tobimatsu, T.; Toraya, T.
Construction and characterization of hybrid dehydratases between adenosylcobalamin-dependent diol and glycerol dehydratases
J. Nutr. Sci. Vitaminol.
53
102-108
2007
Klebsiella oxytoca, Klebsiella pneumoniae
brenda
Kawata, M.; Kinoshita, K.; Takahashi, S.; Ogura, K.; Komoto, N.; Yamanishi, M.; Tobimatsu, T.; Toraya, T.
Survey of Catalytic Residues and Essential Roles of Glutamate-aplpha170 and Aspartate-alpha335 in Coenzyme B12-dependent Diol Dehydratase
J. Biol. Chem.
281
18327-18334
2006
Klebsiella oxytoca
brenda
Tobimatsu, T.; Nishiki, T.; Morimoto, M.; Miyata, R.; Toraya, T.
Low-solubility glycerol dehydratase, a chimeric enzyme of coenzyme B(12)-dependent glycerol and diol dehydratases
Arch. Microbiol.
191
199-206
2008
Salmonella enterica, Klebsiella oxytoca, Klebsiella pneumoniae
brenda
Kinoshita, K.; Kawata, M.; Ogura, K.; Yamasaki, A.; Watanabe, T.; Komoto, N.; Hieda, N.; Yamanishi, M.; Tobimatsu, T.; Toraya, T.
Histidine-alpha143 assists 1,2-hydroxyl group migration and protects radical intermediates in coenzyme B12-dependent diol dehydratase
Biochemistry
47
3162-3173
2008
Klebsiella oxytoca
brenda
Ogura, K.; Kunita, S.; Mori, K.; Tobimatsu, T.; Toraya, T.
Roles of adenine anchoring and ion pairing at the coenzyme B12-binding site in diol dehydratase catalysis
FEBS J.
275
6204-6216
2008
Klebsiella oxytoca
brenda
Toraya, T.; Tamura, N.; Watanabe, T.; Yamanishi, M.; Hieda, N.; Mori, K.
Mechanism-based inactivation of coenzyme B12-dependent diol dehydratase by 3-unsaturated 1,2-diols and thioglycerol
J. Biochem.
144
437-446
2008
Klebsiella oxytoca
brenda
Toraya, T.; Honda, S.; Mori, K.
Coenzyme B12-dependent diol dehydratase is a potassium ion-requiring calcium metalloenzyme: evidence that the substrate-coordinated metal ion is calcium
Biochemistry
49
7210-7217
2010
Klebsiella oxytoca, Klebsiella oxytoca ATCC 8724
brenda
Mori, K.; Hosokawa, Y.; Yoshinaga, T.; Toraya, T.
Diol dehydratase-reactivating factor is a reactivase - evidence for multiple turnovers and subunit swapping with diol dehydratase
FEBS J.
277
4931-4943
2010
Klebsiella oxytoca (Q59470), Klebsiella oxytoca (Q59471), Klebsiella oxytoca (Q59472)
brenda
Kamachi, T.; Doitomi, K.; Takahata, M.; Toraya, T.; Yoshizawa, K.
Catalytic roles of the metal ion in the substrate-binding site of coenzyme B12-dependent diol dehydratase
Inorg. Chem.
50
2944-2952
2011
Klebsiella oxytoca
brenda
Yamanishi, M.; Kinoshita, K.; Fukuoka, M.; Saito, T.; Tanokuchi, A.; Ikeda, Y.; Obayashi, H.; Mori, K.; Shibata, N.; Tobimatsu, T.; Toraya, T.
Redesign of coenzyme B12 dependent diol dehydratase to be resistant to the mechanism-based inactivation by glycerol and act on longer chain 1,2-diols
FEBS J.
279
793-804
2012
Klebsiella oxytoca (Q59470), Klebsiella oxytoca ATCC 8724 (Q59470)
brenda
Shibata, N.; Sueyoshi, Y.; Higuchi, Y.; Toraya, T.
Direct participation of a peripheral side chain of a corrin ring in coenzyme B12 catalysis
Angew. Chem. Int. Ed. Engl.
57
7830-7835
2018
Klebsiella oxytoca (Q59470)
brenda
Toraya, T.; Tanokuchi, A.; Yamasaki, A.; Nakamura, T.; Ogura, K.; Tobimatsu, T.
Diol dehydratase-reactivase is essential for recycling of coenzyme B12 in diol dehydratase
Biochemistry
55
69-78
2016
Klebsiella oxytoca (Q59470 and Q59471 and Q59472), Klebsiella oxytoca, Klebsiella oxytoca ATCC 8724 (Q59470 and Q59471 and Q59472)
brenda
Levin, B.J.; Balskus, E.P.
Characterization of 1,2-propanediol dehydratases reveals distinct mechanisms for B12-dependent and glycyl radical enzymes
Biochemistry
57
3222-3226
2018
Roseburia inulinivorans, Klebsiella oxytoca (Q59470 and Q59471 and Q59472), Roseburia inulinivorans A2-194, Klebsiella oxytoca ATCC 8724 (Q59470 and Q59471 and Q59472)
brenda
Doitomi, K.; Kamachi, T.; Toraya, T.; Yoshizawa, K.
Computational mutation study of the roles of catalytic residues in coenzyme B12-dependent diol dehydratase
Bull. Chem. Soc. JPN
89
955-964
2016
Klebsiella oxytoca (Q59470)
-
brenda