BRENDA - Enzyme Database show
show all sequences of 1.1.1.95

Transient kinetic analysis of the interaction of L-serine with Escherichia coli D-3-phosphoglycerate dehydrogenase reveals the mechanism of V-type regulation and the order of effector binding

Burton, R.L.; Chen, S.; Xu, X.L.; Grant, G.A.; Biochemistry 48, 12242-12251 (2009)

Data extracted from this reference:

Engineering
Amino acid exchange
Commentary
Organism
W139F/E360W
exhibits catalytic activity comparable to that of the native enzyme and is effectively inhibited by L-serine. The only fluorescence signal of the mutant is due to the single tryptophan at position 360. Pre-steady state analysis of binding of inhibitor serine shows that each serine binding interface produces an integrated fluorescent signal
Escherichia coli
Inhibitors
Inhibitors
Commentary
Organism
Structure
L-serine
physiological inhibitor, exerts its effect on at least two steps in the kinetic mechanism. There is a small but significant effect on the dissociation constant of NADH, increasing the Kd to 5 and 23 microM from 0.6 and 9 microM, respectively, for the two sets of sites in the enzyme. After the second substrate is added, serine reduces the amplitude of the signal without a significant effect on the observed rate constants for binding. The serine concentration that reduces the amplitude by 50% is equal to the K0.5 for serine inhibition. Serine binding eliminates a conformational change subsequent to substrate binding by formation of a dead-end quaternary complex consisting of enzyme, coenzyme, substrate, and effector. The rate data conform to a model in which serine can bind to two forms of the enzyme with different affinities
Escherichia coli
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli
P0A9T0
-
-
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2-oxoglutarate + NADH + H+
-
711203
Escherichia coli
2-hydroxyglutarate + NAD+
-
-
-
?
Cofactor
Cofactor
Commentary
Organism
Structure
NADH
-
Escherichia coli
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
NADH
-
Escherichia coli
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
W139F/E360W
exhibits catalytic activity comparable to that of the native enzyme and is effectively inhibited by L-serine. The only fluorescence signal of the mutant is due to the single tryptophan at position 360. Pre-steady state analysis of binding of inhibitor serine shows that each serine binding interface produces an integrated fluorescent signal
Escherichia coli
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
L-serine
physiological inhibitor, exerts its effect on at least two steps in the kinetic mechanism. There is a small but significant effect on the dissociation constant of NADH, increasing the Kd to 5 and 23 microM from 0.6 and 9 microM, respectively, for the two sets of sites in the enzyme. After the second substrate is added, serine reduces the amplitude of the signal without a significant effect on the observed rate constants for binding. The serine concentration that reduces the amplitude by 50% is equal to the K0.5 for serine inhibition. Serine binding eliminates a conformational change subsequent to substrate binding by formation of a dead-end quaternary complex consisting of enzyme, coenzyme, substrate, and effector. The rate data conform to a model in which serine can bind to two forms of the enzyme with different affinities
Escherichia coli
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2-oxoglutarate + NADH + H+
-
711203
Escherichia coli
2-hydroxyglutarate + NAD+
-
-
-
?
Other publictions for EC 1.1.1.95
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)
738070
Deng
-
Construction and characterizat ...
Escherichia coli
Chin. J. Biotechnol.
32
468-477
2016
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737315
Fan
Human phosphoglycerate dehydro ...
Homo sapiens
ACS Chem. Biol.
10
510-516
2015
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737455
Xu
Characterization, modification ...
Corynebacterium glutamicum, Corynebacterium glutamicum SYPS-062
Ann. Microbiol.
65
929-935
2015
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737556
Xu
Comparison of type 1 D-3-phosp ...
Bacillus subtilis, Corynebacterium glutamicum, Homo sapiens, Mycobacterium marinum, Mycobacterium smegmatis, Mycobacterium tuberculosis, Streptomyces coelicolor
Arch. Biochem. Biophys.
570
32-39
2015
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14
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3
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14
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14
14
738401
Mishra
Characterization of pH-induced ...
Entamoeba histolytica
Int. J. Biol. Macromol.
79
284-289
2015
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1
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739236
Deng
Molecular cloning and expressi ...
Acanthamoeba castellanii, Acanthamoeba castellanii ATCC 30011
Parasitol. Res.
114
1387-1395
2015
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726890
Kumar
Crystal structures of type III ...
Pyrococcus horikoshii, Pyrococcus horikoshii DSM 12428, Sulfolobus tokodaii
Biochem. Biophys. Res. Commun.
451
126-130
2014
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2
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737694
Xu
Regulation of Mycobacterium tu ...
Mycobacterium tuberculosis
Biochemistry
53
4239-4249
2014
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738215
Singh
Crystal structures and kinetic ...
Entamoeba histolytica
FEBS J.
281
5498-5512
2014
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2
739512
Wang
Discovery of novel allosteric ...
Escherichia coli
PLoS ONE
9
e94829
2014
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738901
Ehmsen
D-serine in glia and neurons d ...
Mus musculus
J. Neurosci.
33
12464-12469
2013
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2
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739293
Benstein
Arabidopsis phosphoglycerate d ...
Arabidopsis thaliana
Plant Cell
25
5011-5029
2013
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12
1
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15
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12
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12
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739346
Toujani
Functional characterization of ...
Arabidopsis thaliana
Plant Physiol.
163
1164-1178
2013
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1
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739373
Toujani
Identification of the phosphog ...
Arabidopsis thaliana
Plant Signal. Behav.
8
e27207
2013
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2
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725917
Mishra
Glu-108 is essential for subun ...
Entamoeba histolytica
Mol. Biochem. Parasitol.
181
117-124
2012
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724307
Grant
Transient kinetic analysis of ...
Escherichia coli
Biochemistry
50
2900-2906
2011
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696336
Burton
Role of the anion-binding site ...
Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv
Biochemistry
48
4808-4815
2009
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10
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1
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1
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698189
Tabatabaie
Novel mutations in 3-phosphogl ...
Homo sapiens
Hum. Mutat.
30
749-756
2009
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1
-
7
-
1
3
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1
1
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2
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700437
Jeon
Expression of L-serine biosynt ...
Mus musculus
Neurochem. Res.
34
827-834
2009
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700463
Kinoshita
Selective upregulation of 3-ph ...
Mus musculus
Neurosci. Lett.
453
21-26
2009
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701170
Du
3-Phosphoglycerate dehydrogena ...
Homo sapiens, Mus musculus
Reproduction
139
237-245
2009
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2
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2
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711203
Burton
Transient kinetic analysis of ...
Escherichia coli
Biochemistry
48
12242-12251
2009
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684698
Shimizu
Molecular and functional chara ...
Sulfolobus tokodaii
Arch. Biochem. Biophys.
470
120-128
2008
2
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1
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9
6
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1
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2
2
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9
2
6
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1
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1
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686940
Jun
Positive regulation of promote ...
Homo sapiens
Gene
414
106-114
2008
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1
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669548
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Zhao
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Al-Rabiee
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287545
Schuller
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287538
Tobey
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287539
Lund
Purification and subunit struc ...
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Phosphoglycerate dehydrogenase ...
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287541
Anderson
Inactivation of chicken liver ...
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D-3-phosphoglycerate dehydroge ...
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-
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1
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2
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1
1
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287527
Slaughter
3-Phosphoglycerate dehydrogena ...
Pisum sativum
Methods Enzymol.
41
278-281
1975
1
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2
3
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2
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4
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1
1
2
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2
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287528
Feld
D-3-Phosphoglycerate dehydroge ...
Sus scrofa
Methods Enzymol.
41
282-285
1975
-
-
-
-
-
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-
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1
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9
1
1
1
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6
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6
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1
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9
1
1
1
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287529
Rosenblum
D-3-Phosphoglycerate dehydroge ...
Triticum aestivum
Methods Enzymol.
41
285-289
1975
-
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2
1
4
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2
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1
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6
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6
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2
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1
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4
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1
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1
1
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1
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1
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287534
Winicov
Stereospecificity of hydrogen ...
Escherichia coli
Biochim. Biophys. Acta
397
288-293
1975
-
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-
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1
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-
287537
Saski
Regulatory properties of purif ...
Bacillus subtilis
Eur. J. Biochem.
51
415-427
1975
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-
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-
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2
4
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1
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2
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1
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1
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1
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1
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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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287542
Slaughter
-
The amino acid sequence of yea ...
Pisum sativum
Biochem. Soc. Trans.
3
1058-1061
1975
-
-
-
-
-
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2
-
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1
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1
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2
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2
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2
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1
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-
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-
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287536
Slaughter
Inhibition of 3-phosphoglycera ...
Pisum sativum
Biochem. J.
135
563-565
1973
-
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-
-
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6
7
-
1
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2
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1
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1
1
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5
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5
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6
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7
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1
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1
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1
1
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287380
Uhr
Glycine and serine inhibition ...
Rattus norvegicus
FEBS Lett.
17
137-140
1971
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2
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2
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2
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1
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2
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2
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1
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287530
Pizer
-
3-Phosphoglycerate dehydrogena ...
Escherichia coli
Methods Enzymol.
17B
325-331
1971
-
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1
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1
3
3
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1
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1
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1
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1
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2
1
1
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1
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5
-
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5
1
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1
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3
-
3
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1
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1
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1
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2
1
1
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1
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287533
Pizer
Serine biosynthesis and regula ...
Haemophilus influenzae
J. Bacteriol.
97
1357-1361
1969
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1
-
1
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287525
Sugimoto
The mechanism of end product i ...
Escherichia coli
J. Biol. Chem.
243
2081-2089
1968
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1
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9
2
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1
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3
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1
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2
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1
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1
1
1
2
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287531
Sojka
The serine biosynthetic pathwa ...
Neurospora crassa
Biochim. Biophys. Acta
148
42-47
1967
-
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1
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1
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1
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287526
Willis
-
The occurence of D-3-phosphogl ...
Bos taurus, Canis lupus familiaris, Frog, Gallus gallus, Oryctolagus cuniculus, Pigeon, Rattus norvegicus, Sus scrofa
Biochim. Biophys. Acta
81
39-54
1964
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1
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8
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1
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24
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8
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7
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1
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18
-
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18
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1
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1
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24
-
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8
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7
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1
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287532
Umbarger
Biosynthetic pathway of serine ...
Salmonella enterica subsp. enterica serovar Typhimurium
Biochim. Biophys. Acta
62
193-195
1962
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