BRENDA - Enzyme Database show
show all sequences of 1.2.1.59

Structure of Streptococcus agalactiae glyceraldehyde-3-phosphate dehydrogenase holoenzyme reveals a novel surface

Ayres, C.A.; Schormann, N.; Senkovich, O.; Fry, A.; Banerjee, S.; Ulett, G.C.; Chattopadhyay, D.; Acta Crystallogr. Sect. F 70, 1333-1339 (2014)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
recombinant expression of N-terminal His6-tagged enzyme in Escherichia coli strain BL21(DE3)pLysS Rosetta
Streptococcus agalactiae
Crystallization (Commentary)
Crystallization
Organism
purified His-tagged enzyme in complex with NAD+, microseeding method, mixing of 8.9 mg/ml protein in 25 mM HEPES, pH 7.35, 0.1 M NaCl, and 5 mM 2-mercaptoethanol, with crystallization solution containing 26-36% PEG 4000, 0.1 M MES, pH 6.5, the needle-like crystals are used for microseeding by mixing 0.002 ml of protein plus cofactor mixture, 500 nl water and 500 nl reservoir solution containing seed suspension in 28% PEG 4000, 0.1 M MES, pH 6.5, X-ray diffraction structure determination and analysis at 2.46 A resolution, molecular replacement and modelling
Streptococcus agalactiae
Localization
Localization
Commentary
Organism
GeneOntology No.
Textmining
cytosol
-
Streptococcus agalactiae
5829
-
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
D-glyceraldehyde 3-phosphate + phosphate + NAD+
Streptococcus agalactiae
-
3-phospho-D-glyceroyl phosphate + NADH + H+
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
Streptococcus agalactiae NEM316
-
3-phospho-D-glyceroyl phosphate + NADH + H+
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NADP+
Streptococcus agalactiae
-
3-phospho-D-glyceroyl phosphate + NADPH + H+
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NADP+
Streptococcus agalactiae NEM316
-
3-phospho-D-glyceroyl phosphate + NADPH + H+
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Streptococcus agalactiae
Q8E3E8
-
-
Streptococcus agalactiae NEM316
Q8E3E8
-
-
Purification (Commentary)
Commentary
Organism
recombinant N-terminal His6-tagged enzyme from Escherichia coli strain BL21(DE3)pLysS Rosetta by nickel affinity chromatography, ultrafiltration, and gel filtration
Streptococcus agalactiae
Reaction
Reaction
Commentary
Organism
D-glyceraldehyde 3-phosphate + phosphate + NAD(P)+ = 3-phospho-D-glyceroyl phosphate + NAD(P)H + H+
GAPDH catalyzes the oxidative phosphorylation of D-glyceraldehyde 3-phosphate (D-G3H) to give 1,3-diphosphoglyceric acid and uses NAD+ or NADP+ as a cofactor. In the first step of this two-step reaction the active-site cysteine residue of GAPDH attaches covalently to D-G3H and forms a thiohemiacetal intermediate, which transfers a hydride ion to NAD+, resulting in the formation of the thioacyl enzyme. In the second step the resulting thioester is phosphorylated through the nucleophilic attack of an inorganic phosphate ion on the carbonyl C atom of the thioacyl group, which leads to the formation of 1,3-diphosphoglycerate
Streptococcus agalactiae
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
D-glyceraldehyde 3-phosphate + phosphate + NAD+
-
741524
Streptococcus agalactiae
3-phospho-D-glyceroyl phosphate + NADH + H+
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
-
741524
Streptococcus agalactiae NEM316
3-phospho-D-glyceroyl phosphate + NADH + H+
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NADP+
-
741524
Streptococcus agalactiae
3-phospho-D-glyceroyl phosphate + NADPH + H+
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NADP+
-
741524
Streptococcus agalactiae NEM316
3-phospho-D-glyceroyl phosphate + NADPH + H+
-
-
-
?
Subunits
Subunits
Commentary
Organism
tetramer
crystal structure analysis
Streptococcus agalactiae
Cofactor
Cofactor
Commentary
Organism
Structure
additional information
GAPDH catalyzes the oxidative phosphorylation of D-glyceraldehyde 3-phosphate using NAD+ or NADP+ as a cofactor
Streptococcus agalactiae
NAD+
enzyme binding structure analysis
Streptococcus agalactiae
NADP+
-
Streptococcus agalactiae
Cloned(Commentary) (protein specific)
Commentary
Organism
recombinant expression of N-terminal His6-tagged enzyme in Escherichia coli strain BL21(DE3)pLysS Rosetta
Streptococcus agalactiae
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
additional information
GAPDH catalyzes the oxidative phosphorylation of D-glyceraldehyde 3-phosphate using NAD+ or NADP+ as a cofactor
Streptococcus agalactiae
NAD+
enzyme binding structure analysis
Streptococcus agalactiae
NADP+
-
Streptococcus agalactiae
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified His-tagged enzyme in complex with NAD+, microseeding method, mixing of 8.9 mg/ml protein in 25 mM HEPES, pH 7.35, 0.1 M NaCl, and 5 mM 2-mercaptoethanol, with crystallization solution containing 26-36% PEG 4000, 0.1 M MES, pH 6.5, the needle-like crystals are used for microseeding by mixing 0.002 ml of protein plus cofactor mixture, 500 nl water and 500 nl reservoir solution containing seed suspension in 28% PEG 4000, 0.1 M MES, pH 6.5, X-ray diffraction structure determination and analysis at 2.46 A resolution, molecular replacement and modelling
Streptococcus agalactiae
Localization (protein specific)
Localization
Commentary
Organism
GeneOntology No.
Textmining
cytosol
-
Streptococcus agalactiae
5829
-
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
D-glyceraldehyde 3-phosphate + phosphate + NAD+
Streptococcus agalactiae
-
3-phospho-D-glyceroyl phosphate + NADH + H+
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
Streptococcus agalactiae NEM316
-
3-phospho-D-glyceroyl phosphate + NADH + H+
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NADP+
Streptococcus agalactiae
-
3-phospho-D-glyceroyl phosphate + NADPH + H+
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NADP+
Streptococcus agalactiae NEM316
-
3-phospho-D-glyceroyl phosphate + NADPH + H+
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant N-terminal His6-tagged enzyme from Escherichia coli strain BL21(DE3)pLysS Rosetta by nickel affinity chromatography, ultrafiltration, and gel filtration
Streptococcus agalactiae
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
D-glyceraldehyde 3-phosphate + phosphate + NAD+
-
741524
Streptococcus agalactiae
3-phospho-D-glyceroyl phosphate + NADH + H+
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
-
741524
Streptococcus agalactiae NEM316
3-phospho-D-glyceroyl phosphate + NADH + H+
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NADP+
-
741524
Streptococcus agalactiae
3-phospho-D-glyceroyl phosphate + NADPH + H+
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NADP+
-
741524
Streptococcus agalactiae NEM316
3-phospho-D-glyceroyl phosphate + NADPH + H+
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
tetramer
crystal structure analysis
Streptococcus agalactiae
General Information
General Information
Commentary
Organism
physiological function
the enzyme plays a key role in glycolysis. GAPDH localized on the surface of some bacteria is thought to be involved in macromolecular interactions and bacterial pathogenesis. GAPDH on the surface of group B streptococcus (GBS) enhances bacterial virulence and is a potential vaccine candidate
Streptococcus agalactiae
General Information (protein specific)
General Information
Commentary
Organism
physiological function
the enzyme plays a key role in glycolysis. GAPDH localized on the surface of some bacteria is thought to be involved in macromolecular interactions and bacterial pathogenesis. GAPDH on the surface of group B streptococcus (GBS) enhances bacterial virulence and is a potential vaccine candidate
Streptococcus agalactiae
Other publictions for EC 1.2.1.59
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)
741524
Ayres
Structure of Streptococcus ag ...
Streptococcus agalactiae, Streptococcus agalactiae NEM316
Acta Crystallogr. Sect. F
70
1333-1339
2014
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1
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743222
Bommareddy
A de novo NADPH generation pa ...
Corynebacterium glutamicum, Corynebacterium glutamicum ATCC13032
Metab. Eng.
25
30-37
2014
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1
1
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6
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9
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1
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1
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10
10
743026
Jiang
Metabolic engineering of Cory ...
Clostridium acetobutylicum
J. Ind. Microbiol. Biotechnol.
40
1143-1151
2013
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725013
Ito
Comparative analysis of two gl ...
Sulfurisphaera tokodaii, Sulfurisphaera tokodaii 7
FEBS Lett.
586
3097-3103
2012
1
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1
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7
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723857
Tourigny
Expression, purification, crys ...
Campylobacter jejuni, Campylobacter jejuni NCTC 11168
Acta Crystallogr. Sect. F
67
72-75
2011
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1
1
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725853
Kim
Alteration of reducing powers ...
Bacillus subtilis 168, Bacillus subtilis
Lett. Appl. Microbiol.
52
433-440
2011
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726605
Malay
Structure of glyceraldehyde-3- ...
Methanocaldococcus jannaschii, Methanocaldococcus jannaschii DSM 2661
Acta Crystallogr. Sect. F
65
1227-1233
2009
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1
1
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656414
Marri
Co-ordinated gene expression o ...
Arabidopsis thaliana
J. Exp. Bot.
56
73-80
2005
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1
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11538
Valverde
Functional complementation of ...
Anabaena sp., Calothrix sp., Fischerella sp., Fischerella sp. UTEX 1829, Methanobacterium bryantii, Methanobacterium formicicum, Methanothermus fervidus, Nostoc sp., Pseudanabaena sp., Pseudanabaena sp. PCC6903, Stanieria sp., Synechococcus sp., Synechocystis sp.
J. Bacteriol.
179
4513-4522
1997
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17
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28
2
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28
2
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1
1
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11542
Serrano
-
Identification of two differen ...
Cyanophora paradoxa
Arch. Microbiol.
162
14-19
1994
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744178
Schäfer
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Gluconeogenesis from pyruvate ...
Pyrococcus furiosus
Arch. Microbiol.
159
354-363
1993
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11537
Zwickl
Glyceraldehyde-3-phosphate deh ...
Pyrococcus woesei
J. Bacteriol.
172
4329-4338
1990
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11539
Fabry
Purification and characterizat ...
Methanothermus fervidus
Eur. J. Biochem.
165
147-155
1987
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11541
Papen
-
Properties of the glyceraldehy ...
Anabaena cylindrica, Anabaena sp., Anabaena sp. 7119, Trichormus variabilis
FEMS Microbiol. Lett.
36
201-206
1986
9
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11540
Krusteva
-
Allosteric regulation of NAD(N ...
Auxenochlorella pyrenoidosa
FEBS Lett.
171
137-140
1984
6
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