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Literature summary for 2.7.2.3 extracted from

  • Palmai, Z.; Chaloin, L.; Lionne, C.; Fidy, J.; Perahia, D.; Balog, E.
    Substrate binding modifies the hinge bending characteristics of human 3-phosphoglycerate kinase: A molecular dynamics study (2009), Proteins Struct. Funct. Bioinform., 77, 319-329.
    View publication on PubMed
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Organism

Organism UniProt Comment Textmining
Homo sapiens
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Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
ADP + 3-phospho-D-glyceroyl 1-phosphate molecular dynamics simulations reveal, that both in the absence and in the presence of ligands the enzyme exhibits a hinge bending type motion but the characteristics of this motion vary considerably. In the apo form, the enzyme exhibits a hinge bending motion of a relatively small amplitude with a time period around 20 ns while the time period of the complexed form is much longer than simulation time. In both cases there is a hinge at the C-terminal side of helix 7, but the hinge points which are near the substrate binding site change upon binding. The apo form is more flexible, there are more hinge points that contribute with similar significance to the hinge bending motion, while in the ternary complex there is only one dominant hinge point. This is located in the vicinity of the substrates, in loop K13. The binding of ADP rigidifies its binding site in the C-domain, while binding 1,3-diphosphoglycerate increases the flexibility of the binding range of the N-domain Homo sapiens ATP + 3-phospho-D-glycerate
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Synonyms

Synonyms Comment Organism
3-phosphoglycerate kinase
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 Homo sapiens
PGK
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 Homo sapiens

Cofactor

Cofactor Comment Organism Structure
ADP
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 Homo sapiens