BRENDA - Enzyme Database
show all sequences of 5.1.1.4

The Catalytic Activity of Proline Racemase: A Quantum Mechanical/Molecular Mechanical Study

Stenta, M.; Calvaresi, M.; Altoe, P.; Spinelli, D.; Garavelli, M.; Bottoni, A.; J. Phys. Chem. B 112, 1057-1059 (2008)

Data extracted from this reference:

Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Trypanosoma cruzi
Q4DA80
-
-
Trypanosoma cruzi
-
-
-
Reaction
Reaction
Commentary
Organism
L-proline = D-proline
a new combined quantum mechanical and molecular mechanical (QM/MM) potential to study the reaction mechanism of proline racemase is used. Three critical points are identified: two almost isoenergetic minima (M1a and M2a), in which the enzyme is bound to L- and D-Pro, respectively, and a transition state (TSCa), unveiling a highly asynchronous concerted process; quantum mechanical and molecular mechanical study reveals two almost isoenergetic minima M1a and M2a, in which the enzyme is bound to L-proline and D-proline, respectively, and a transition state TSCa, unveiling a highly asynchronous concerted process. Residues Asn133, Asp296, and Gly301 destabilize M2a. Conversely, both Gly131and Gly303 stabilize M2a. Residues Gly131, Gly301, and Thr302 stabilize TSCa
Trypanosoma cruzi
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
L-proline
-
675621
Trypanosoma cruzi
D-proline
-
-
-
?
additional information
quantum mechanical and molecular mechanical study reveals two almost isoenergetic minima M1a and M2a, in which the enzyme is bound to L-proline and D-proline, respectively, and a transition state TSCa, unveiling a highly asynchronous concerted process. Residues Asn133, Asp296, and Gly301 destabilize M2a. Conversely, both Gly131 and Gly303 stabilize M2a. Residues Gly131, Gly301, and Thr302 stabilize TSCa
675621
Trypanosoma cruzi
?
-
-
-
-
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
L-proline
-
675621
Trypanosoma cruzi
D-proline
-
-
-
?
additional information
quantum mechanical and molecular mechanical study reveals two almost isoenergetic minima M1a and M2a, in which the enzyme is bound to L-proline and D-proline, respectively, and a transition state TSCa, unveiling a highly asynchronous concerted process. Residues Asn133, Asp296, and Gly301 destabilize M2a. Conversely, both Gly131 and Gly303 stabilize M2a. Residues Gly131, Gly301, and Thr302 stabilize TSCa
675621
Trypanosoma cruzi
?
-
-
-
-
Other publictions for EC 5.1.1.4
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)
730678
Watanabe
Identification and characteriz ...
Clostridioides difficile, Ferroplasma acidarmanus, Haloarcula japonica, Haloarcula japonica DSM 6131, Thermococcus litoralis, Thermococcus litoralis DSM 5473
PLoS One
10
e0120349
2015
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4
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2
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4
15
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8
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12
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4
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12
4
8
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15
4
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4
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4
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2
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4
4
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15
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8
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4
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12
4
8
-
-
15
4
-
-
-
-
-
-
-
15
15
748829
Caballero
Phylogenetic and syntenic dat ...
no activity in Trypanosoma brucei, no activity in Trypanosoma congolense, Trypanosoma conorhini, Trypanosoma conorhini TCC025, Trypanosoma cruzi, Trypanosoma cruzi CL Brener, Trypanosoma cruzi marinkellei, Trypanosoma cruzi marinkellei TCC344, Trypanosoma dionisii, Trypanosoma dionisii TCC211, Trypanosoma erneyi, Trypanosoma erneyi TCC1946, Trypanosoma grayi, Trypanosoma grayi ANR4, Trypanosoma lewisi, Trypanosoma lewisi TCC034, Trypanosoma rangeli, Trypanosoma serpentis, Trypanosoma serpentis TCC1052, Trypanosoma sp., Trypanosoma sp. TCC1825 / RCF-2014, Trypanosoma sp. TCC339, Trypanosoma sp. TCC878, Trypanosoma sp. TCC878 RCF-2014, Trypanosoma vivax, Trypanosoma vivax Y486
Parasit. Vectors
8
222
2015
-
-
13
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47
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14
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-
13
14
-
-
-
727156
Harty
Inhibition of serine and proli ...
Acetoanaerobium sticklandii
Bioorg. Med. Chem. Lett.
24
390-393
2014
-
-
1
-
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-
4
1
-
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1
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3
-
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1
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1
1
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1
1
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2
4
1
1
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1
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1
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2
-
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-
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-
1
1
-
-
-
727265
Wu
The Clostridium difficile prol ...
Clostridioides difficile
Can. J. Microbiol.
60
251-254
2014
-
-
-
-
-
-
-
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3
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-
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-
-
-
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-
-
1
1
-
-
-
749144
Fikru
A proline racemase based PCR ...
Trypanosoma vivax, Trypanosoma vivax ILRAD 1392
PLoS ONE
9
e84819
2014
-
1
-
-
1
-
-
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15
-
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2
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2
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-
728600
Berneman
Combined approaches for drug d ...
Trypanosoma cruzi
PLoS ONE
8
e60955
2013
-
-
1
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-
9
-
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1
-
4
-
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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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9
6
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1
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1
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1
-
1
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1
-
-
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-
-
-
715163
Bryan
Genetic immunization converts ...
Trypanosoma cruzi, Trypanosoma cruzi Y
Infect. Immun.
78
810-822
2010
-
-
1
-
-
-
-
-
-
-
1
-
-
12
-
-
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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-
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1
1
-
-
-
704196
Rubinstein
Catalyzing racemizations in th ...
Trypanosoma cruzi
J. Am. Chem. Soc.
131
8513-8521
2009
-
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1
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1
1
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-
-
-
-
-
-
-
-
-
-
-
704292
Fonknechten
A conserved gene cluster rules ...
Acetoanaerobium sticklandii
J. Bacteriol.
191
3162-3167
2009
-
-
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1
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1
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1
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1
1
-
-
-
705499
Coutinho
Inhibition of Trypanosoma cruz ...
Trypanosoma cruzi
Mem. Inst. Oswaldo Cruz
104
1055-1062
2009
-
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1
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1
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2
1
1
2
-
-
705500
Coatnoan
Proline racemases: Insights in ...
Trypanosoma cruzi
Mem. Inst. Oswaldo Cruz
104
295-300
2009
-
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1
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4
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2
2
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1
1
2
2
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705596
Chamond
Proline racemases are conserve ...
Trypanosoma vivax
Mol. Biochem. Parasitol.
165
170-179
2009
-
1
1
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1
2
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1
1
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7
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1
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3
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1
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675621
Stenta
The Catalytic Activity of Prol ...
Trypanosoma cruzi
J. Phys. Chem. B
112
1057-1059
2008
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676749
Goytia
Molecular and structural discr ...
Clostridioides difficile, Clostridioides difficile VPI10463
PLoS ONE
2
e885
2007
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1
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2
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7
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676832
Buschiazzo
Crystal structure, catalytic m ...
Trypanosoma cruzi
Proc. Natl. Acad. Sci. USA
103
1705-1710
2006
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1
1
2
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1
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1
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662908
Chamond
Trypanosoma cruzi proline race ...
Trypanosoma cruzi
Mol. Microbiol.
58
46-60
2005
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2
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652377
Chamond
Biochemical characterization o ...
Trypanosoma cruzi
J. Biol. Chem.
278
15484-15494
2003
-
1
1
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1
2
3
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3
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6
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5
3
1
1
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1
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2
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1
1
1
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5
3
1
1
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1
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653295
Reina-San-Martin
A B-cell mitogen from a pathog ...
Trypanosoma cruzi
Nat. Med.
6
890-897
2000
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2125
Fisher
Energetics of proline racemase ...
Acetoanaerobium sticklandii
Biochemistry
25
2529-2537
1986
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2126
Fisher
Energetics of proline racemase ...
Acetoanaerobium sticklandii
Biochemistry
25
2543-2551
1986
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2127
Belasco
Energetics of proline racemase ...
Acetoanaerobium sticklandii
Biochemistry
25
2564-2571
1986
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2128
Fisher
Energetics of proline racemase ...
Acetoanaerobium sticklandii
Biochemistry
25
2538-2542
1986
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2129
Belasco
Energetics of proline racemase ...
Acetoanaerobium sticklandii
Biochemistry
25
2558-2564
1986
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1
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2130
Albery
Energetics and mechanism of pr ...
Acetoanaerobium sticklandii
Biochemistry
25
2572-2577
1986
-
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1
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1
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2131
Belasco
Energetics of proline racemase ...
Acetoanaerobium sticklandii
Biochemistry
25
2552-2558
1986
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1
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1
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2124
Rudnick
Reaction mechanism and structu ...
Acetoanaerobium sticklandii
Biochemistry
14
4515-4522
1975
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3
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1
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2
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1
1
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1
1
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3
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1
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1
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1
1
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2123
Keenan
The inhibition of proline race ...
Acetoanaerobium sticklandii
Biochem. Biophys. Res. Commun.
57
500-504
1974
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1
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2122
Cardinale
Purification and mechanism of ...
Acetoanaerobium sticklandii
Biochemistry
7
3970-3978
1968
3
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18
2
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1
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1
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1
1
1
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1
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3
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18
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2
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1
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1
1
1
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1
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2121
Stadtman
Studies on the enzymic reducti ...
Acetoanaerobium sticklandii
J. Biol. Chem.
228
983-997
1957
3
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3
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