3gon | pdb_00003gon

Streptococcus pneumoniae Phosphomevalonate Kinase in Complex with Phosphomevalonate and AMPPNP

spinqualitylabelsall models 3gon, resolution 1.90Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3gon is a 1 chain structure with sequence from Strr6. This structure supersedes the now removed PDB entry 2pg9. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ANP, MG, PMV Gene: mvaK2, spr0340 (STRR6) Activity: Phosphomevalonate kinase, with EC number 2.7.4.2 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed The galacto-, homoserine-, mevalonate-, phosphomevalonate-kinase (GHMP) superfamily encompases a wide-range of protein function. Three members of the family (mevalonate kinase, phosphomevalonate kinase, and diphosphomevalonate decarboxylase) comprise the mevalonate pathway found in S. pneumoniae and other organisms. We have determined the 1.9 A crystal structure of phosphomevalonate kinase (PMK) from S. pneumoniae in complex with phosphomevalonate and AMPPNP.Mg(2+). Comparison of the apo and ternary PMK structures suggests that 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. Analysis of all available GHMP kinase ternary complex structures reveals that while their C(alpha)-scaffolds are highly conserved, their substrates bind in one of two conformations, which appear to be either reactive or nonreactive. 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 ordered water, which clusters near the charged regions of the substrate. Notably, a water pentamer that interacts extensively with the reactive groups of both substrates was discovered at the active site. Structure of the ternary complex of phosphomevalonate kinase: the enzyme and its family.,Andreassi JL 2nd, Vetting MW, Bilder PW, Roderick SL, Leyh TS Biochemistry. 2009 Jul 14;48(27):6461-8. PMID:19485344 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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