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Literature summary for 1.2.1.12 extracted from

  • Zhou, K.; Fan, X.; Li, Y.; Zhang, C.; Jin, T.
    High-resolution crystal structure of Streptococcus agalactiae glyceraldehyde-3-phosphate dehydrogenase (2018), Acta Crystallogr. Sect. F, 74, 236-244 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
gene gapA, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) CodonPlus RIPL Streptococcus agalactiae ATCC BAA-23

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant detagged group B streptococcus GAPDH enzyme, hanging drop vapour diffusion method, mixing of 20 mg/ml protein in 20 mM Tris-HCl, pH 8.0, and 100 mM NaCl, with reservoir solution containing 2 M ammonium sulfate, 1 M lithium sulfate, and 0.1 M Tris-HCl pH 8.5, cryoprotection by addition of 5% glycerol, X-ray diffraction structure determination and analysis at 1.36 A resolution, molecular replacement using the published structure of GAPDH as a search model (PDB ID 4qx6) Streptococcus agalactiae ATCC BAA-23

Metals/Ions

Metals/Ions Comment Organism Structure
additional information the apo subunit D of the enzyme's crystal structure contains three sulfate ions labelled SUL1, SUL2 and SUL3. SUL1 binds to Ser151, Thr212 and Gly213 by hydrogen bonds. The location of SUL2 is similar to the position of the sulfate ion in subunit A, and the residues to which SUL2 binds by hydrogen bonds are identical to those in subunit A, including Thr182, Arg199 and Arg235. In addition, SUL3 is hydrogen-bonded to the backbone amino group of Arg12. The anion-binding sites located by sulfate ions in our structure could naturally be occupied by phosphate ions Streptococcus agalactiae ATCC BAA-23

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
D-glyceraldehyde 3-phosphate + phosphate + NAD+ Streptococcus agalactiae ATCC BAA-23
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3-phospho-D-glyceroyl phosphate + NADH + H+
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+ Streptococcus agalactiae ATCC BAA-23 ATCC BAA-611
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3-phospho-D-glyceroyl phosphate + NADH + H+
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+ Streptococcus agalactiae ATCC BAA-23 2603V/R
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3-phospho-D-glyceroyl phosphate + NADH + H+
-
?

Organism

Organism UniProt Comment Textmining
Streptococcus agalactiae ATCC BAA-23 Q8DXS8 Group B Streptococcus, GBS
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Streptococcus agalactiae ATCC BAA-23 2603V/R Q8DXS8 Group B Streptococcus, GBS
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Streptococcus agalactiae ATCC BAA-23 ATCC BAA-611 Q8DXS8 Group B Streptococcus, GBS
-

Purification (Commentary)

Purification (Comment) Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) CodonPlus RIPL by nickel affinity chormatography, His-tag cleavage by TEV protease Streptococcus agalactiae ATCC BAA-23

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
D-glyceraldehyde 3-phosphate + phosphate + NAD+
-
Streptococcus agalactiae ATCC BAA-23 3-phospho-D-glyceroyl phosphate + NADH + H+
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
-
Streptococcus agalactiae ATCC BAA-23 ATCC BAA-611 3-phospho-D-glyceroyl phosphate + NADH + H+
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
-
Streptococcus agalactiae ATCC BAA-23 2603V/R 3-phospho-D-glyceroyl phosphate + NADH + H+
-
?

Subunits

Subunits Comment Organism
More the enzyme crystal structure contains an asymmetric mixed holo tetramer (four copies of the GAPDH molecule in one asymmetric unit that form a tetramer or two dimers, namely the A-B dimer and the C-D dimer), with two NAD+ ligands bound to two protomers. The asymmetric dimers A-B of both structures can be aligned nearly perfectly, while the asymmetric dimers C-D are in very different conformations because of the different NAD+ binding states of the molecules. The molecular interfaces within both tetramers are essentially the same. Overall, the two tetramers are in different conformations owing to the different ligand-binding states of the four promoters Streptococcus agalactiae ATCC BAA-23
tetramer 4 * 37000, dimer of dimer, SDS-PAGE Streptococcus agalactiae ATCC BAA-23

Synonyms

Synonyms Comment Organism
GapA
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Streptococcus agalactiae ATCC BAA-23
GAPDH
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Streptococcus agalactiae ATCC BAA-23
GBS GAPDH
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Streptococcus agalactiae ATCC BAA-23
glyceraldehyde-3-phosphate dehydrogenase
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Streptococcus agalactiae ATCC BAA-23

Cofactor

Cofactor Comment Organism Structure
NAD+ enzyme binding structure analysis. Subunit A contains a NAD+ molecule and a sulfate ion in the holo state. The NAD-binding site located in the N-terminal domain. The O atom of the nicotinamide ribose of NAD is hydrogen-bonded to the hydroxyl group in the side chain of Thr121. The NAD+ diphosphate moiety binds to the main chain of the protein with hydrogen bonds from the backbone amino groups of Arg12 and Ile13. The two hydroxyl groups of the adenosine ribose of the NAD+ are hydrogen-bonded to Asp34, and Arg78 forms a hydrogen bond to the amide group of the adenine base Streptococcus agalactiae ATCC BAA-23

General Information

General Information Comment Organism
metabolism glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is the sixth enzyme in the glycolytic pathway, in which it converts D-glyceraldehyde 3-phosphate (D-G3P) to 1,3-bisphosphoglycerate and consumes inorganic phosphate using NAD+ as a coenzyme Streptococcus agalactiae ATCC BAA-23
additional information phosphate ion-binding sites structure analysis. Superimposition of GBS GAPDH and a ternary complex of GBS GAPDH (PDB ID 5jya), structure comparisons of ligand-binding state and of ternary complex enzyme and apoenzyme, implications for the catalytic mechanism, overview Streptococcus agalactiae ATCC BAA-23
physiological function glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a multifunctional enzyme that plays critical roles in bacterial pathogenesis in some pathogenic bacteria Streptococcus agalactiae ATCC BAA-23