Any feedback?
Please rate this page
(literature.php)
(0/150)

BRENDA support

Literature summary extracted from

  • Andreassi, J.L.; Vetting, M.W.; Bilder, P.W.; Roderick, S.L.; Leyh, T.S.
    Structure of the ternary complex of phosphomevalonate kinase: the enzyme and its family (2009), Biochemistry, 48, 6461-6468.
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.7.4.2 enzyme in a ternary complex with phosphomevalonate, AMPPNP, and Mg2+, by sitting drop method, mixing 0.002 ml of 12 mg/ml PMK in 25 mM HEPES/K+, pH 7.5, 0.25 mM phosphomevalonate, 8 mM AMPPNP, 10 mM MgCl2, with 0.002 ml of 36% w/v PEG 4000, and 100 mM MES/Na+, pH 6.0, X-ray diffraction structure determination and analysis at 1.9 A resolution, molecular replacement with EPMR Streptococcus pneumoniae

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.7.4.2 Mg2+ ligand binding reverses the side-chain orientations of two antiparallel lysines residues 100 and 101 with the result that Lys101 is switched into a position in which its ammonium ion is in direct contact with the beta,gamma-bridging atom of the nucleotide, where it is expected to stabilize both the ground and transition states of the reaction Streptococcus pneumoniae

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.7.4.2 ATP + (R)-5-phosphomevalonate Streptococcus pneumoniae
-
ADP + (R)-5-diphosphomevalonate
-
ir

Organism

EC Number Organism UniProt Comment Textmining
2.7.4.2 Streptococcus pneumoniae
-
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.7.4.2 ATP + (R)-5-phosphomevalonate
-
Streptococcus pneumoniae ADP + (R)-5-diphosphomevalonate
-
ir
2.7.4.2 ATP + (R)-5-phosphomevalonate active site structure and substrate binding coformation, detailed overview. Ligand binding reverses the side-chain orientations of two antiparallel lysines residues 100 and 101 with the result that Lys101 is switched into a position in which its ammonium ion is in direct contact with the beta,gamma-bridging atom of the nucleotide, where it is expected to stabilize both the ground and transition states of the reaction. The active site of PMK seems spacious enough to accommodate interconversion of the reactive and nonreactive conformers. A substantial fraction of the PMK active site is occupied by an active site water pentamer, which clusters near the charged regions of the substrate Streptococcus pneumoniae ADP + (R)-5-diphosphomevalonate
-
ir
2.7.4.2 additional information binding structure of AMPPNP, that interactswith both stationary and mobile regions of the PMK scaffold. The stationary region includes Ile65 and Leu66 as well as the glycine/serine-rich region, F102GLGSSGLV110, of motif II Streptococcus pneumoniae ?
-
?

Synonyms

EC Number Synonyms Comment Organism
2.7.4.2 More phosphomevalonate-kinase belongs to the GHMP superfamily Streptococcus pneumoniae