Primary Citation PubMed: 9519410
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In silico evidence for functional specialization after genome duplication in yeast.
(2009) FEMS Yeast Res 9
PubMed: 19133069 | PubMedCentral: PMC2704937 | DOI: 10.1111/j.1567-1364.2008.00451.x
The crystal structure of CDC19 has been determined complexed with the allosteric regulator fructose-1,6-biphosphate (FBP) and substrate analog (1a3w).
Publication Year: 2009
Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria.
(2013) PLoS Comput Biol 9
PubMed: 23946717 | PubMedCentral: PMC3738050 | DOI: 10.1371/journal.pcbi.1003159
Residues V400 to V411, K446 to F470 and S481 to Q496 of the crystallographically resolved Saccharomyces cerevisiae PYK (PDB id: 1A3W, chain A) are shown in cartoon representation.
Two additional crystallographically resolved structures, namely for Saccharomyces cerevisiae PYK (PDB id: 1A3W) and human PYK M2 (PDB id: 3GR4)  , were selected for the structural comparison of the allosteric activator binding sites.
The crystal structures of the PYKs from Saccharomyces cerevisiae (PDB id: 1A3W) and Homo sapiens (PDB id: 3GR4) were selected as additional reference structures for the structural comparison  .
Panel A shows a section of the crystallographically resolved Saccharomyces cerevisiae PYK (PDB id: 1A3W, chain A) in cartoon representation with the activator FBP bound in the allosteric site in stick representation.
The residues marked in orange correspond to the residues that interact with the allosteric ligand, FBP, in the Saccharomyces cerevisiae PYK (1A3W).
In the yeast and the human M2-type PYKs, the side chains of tryptophan (W452 in 1A3W and W482 in 3GR4) and arginine (R459 in 1A3W and R489 in 3GR4) residues are computed to interact with the 6′-phosphate moiety of FBP (see Figure 1 ).
The Saccharomyces cerevisiae PYK structure (1A3W) was solved with a resolution of 3 Å, and shows a homodimer in the asymmetric unit with open allosteric sites and FBP bound.
We applied Pfinder to the structures Saccharomyces cerevisiae PYK (1A3W), Escherichia coli PYK (1PKY) and the modelled structures.
The second cluster is formed by the electrostatic potentials computed for the template (chim_temp) and the reference crystal structures (1PKY, 1A3W).
Figure 1 shows the allosteric site of Saccharomyces cerevisiae PYK (1A3W) with FBP bound in the activator binding site and the computed phosphate interaction sites.
Publication Year: 2013
Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures.
(2013) BMC Bioinformatics 14 Suppl 16
PubMed: 24564522 | PubMedCentral: PMC3853090 | DOI: 10.1186/1471-2105-14-S16-S2
Figure 4 A case study of phosphorylation sites prediction on the protein structure of Pyruvate kinase 1 (PDB ID: 1A3W) .
Two case studies of kinase-specific phosphorylation sites prediction on protein 3D structures of Pyruvate kinase 1 (PDB ID: 1A3W) and Histone (PDB ID: 2CV5) are presented in Figure 4 and 5 , respectively.
PubMed ID is not available.
Published in 2014
In Results/Discussion, Section “Lactic acid bacteria PYKs lack a second phosphate binding site in the activator binding site”, paragraph 1, 2nd sentence: In the yeast and the human M2-type PYKs, the side chains of tryptophan (W452 in 1A3W and W482 in 3GR4) and arginine (R459 in 1A3W and R489 in 3GR4) residues are computed to interact with the 1′-phosphate moiety of FBP (see Figure 1 ).
Publication Year: 2014
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