Triose Phosphate Isomerase: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 22: | Line 22: | ||
[[Image:classical2.png|left|thumb|500px| '''Classic Mechanism proposed by Knowles and co-workers''']] | [[Image:classical2.png|left|thumb|500px| '''Classic Mechanism proposed by Knowles and co-workers''']] | ||
{{Clear}} | |||
TPI carries out the isomerization reaction through an acid-base-mediated mechanism involving <scene name='Triose_Phosphate_Isomerase/Three_catalytic_residues1/4'>three catalytic residues</scene>, each of which <scene name='Triose_Phosphate_Isomerase/Three_catalytic_residues2/2'>contacts the substrate</scene>. First, the DHAP or GAP substrate is initially attracted to the enzyme active site through '''electrostatic interactions''' between the negatively charged phosphate group of the substrate and the positively charged '''Lys12''', with the resulting interaction stabilizing the substrate. | TPI carries out the isomerization reaction through an acid-base-mediated mechanism involving <scene name='Triose_Phosphate_Isomerase/Three_catalytic_residues1/4'>three catalytic residues</scene>, each of which <scene name='Triose_Phosphate_Isomerase/Three_catalytic_residues2/2'>contacts the substrate</scene>. First, the DHAP or GAP substrate is initially attracted to the enzyme active site through '''electrostatic interactions''' between the negatively charged phosphate group of the substrate and the positively charged '''Lys12''', with the resulting interaction stabilizing the substrate. | ||
According to the "classic" mechanism, '''Glu165''' plays the role of the '''general base''' catalyst by abstracting a proton from the pro(''R'') position of carbon 1 of DHAP or the C-2 proton of GAP. However, the carboxylate group of Glutamate 165 alone does not possess the basicity to abstract a proton and requires | According to the "classic" mechanism, '''Glu165''' plays the role of the '''general base''' catalyst by abstracting a proton from the pro(''R'') position of carbon 1 of DHAP or the C-2 proton of GAP. However, the carboxylate group of Glutamate 165 alone does not possess the basicity to abstract a proton and requires | ||
| Line 85: | Line 87: | ||
Due to its role in the glycolysis, an essential energy-yielding process to many organisms, TPI has been isolated and crystallized from several species. This information has afforded extensive multiple alignment ''in silico'' experiments which subsequently provided <scene name='Triose_Phosphate_Isomerase/Conserved1/1'>amino acid conservation structures</scene> of TPI. <ref>PMID:12403619</ref> Collectively, these tools have determined that --> | Due to its role in the glycolysis, an essential energy-yielding process to many organisms, TPI has been isolated and crystallized from several species. This information has afforded extensive multiple alignment ''in silico'' experiments which subsequently provided <scene name='Triose_Phosphate_Isomerase/Conserved1/1'>amino acid conservation structures</scene> of TPI. <ref>PMID:12403619</ref> Collectively, these tools have determined that --> | ||
TPI has a roughly 50% sequence conservation from bacteria to humans.<ref>PMID:8130194</ref> The <scene name='Triose_Phosphate_Isomerase/Conserved1/ | TPI has a roughly 50% sequence conservation from bacteria to humans.<ref>PMID:8130194</ref> The <scene name='Triose_Phosphate_Isomerase/Conserved1/2'>3D pattern of amino acid conservation</scene> ([[2ypi]]) shows dramatic conservation around the catalytic site. Glu104 is also highly conserved, as are several residues in the [[#Why is the enzyme an obligate dimer?|interdigitating loop]]. Curiously, two Arg residues on the surface, distant from the dimer contact and the catalytic side, are also highly conserved. (See note about the conservation calculation<ref>The conservation pattern shown was calculated by [[ConSurfDB_vs._ConSurf|ConSurfDB]] and might obscure some conservation due to [[Evolutionary_Conservation#ConSurf-DB_Often_Obscures_Some_Functional_Sites|inclusion of proteins of different functions]]. However in the case of [[2ypi]], all sequences used in the multiple sequence alignment were TPI sequences. A manual run at the ConSurf Server, using 500 TPI sequences, gave a nearly identical result. Both runs gave an average pairwise distance close to 1.0. Hence, the conservation pattern shown is correct for TPI.</ref>.) | ||
One specific example of sequence homology is that of loop 6 and loop 7 residues, whose structural contributions are discussed above. In a sequence alignment of 133 TIM sequences, two highly conserved motifs are noticed. First, 114 sequences in loop 6 contain the PXW sequence family (where X is I,L or V in 112 sequences or otherwise a T or K). Secondly, loop 7 contains a highly conserved YGGS motif; however, this motif is only found when the N-terminal hinge contains tryptophan. | One specific example of sequence homology is that of loop 6 and loop 7 residues, whose structural contributions are discussed above. In a sequence alignment of 133 TIM sequences, two highly conserved motifs are noticed. First, 114 sequences in loop 6 contain the PXW sequence family (where X is I,L or V in 112 sequences or otherwise a T or K). Secondly, loop 7 contains a highly conserved YGGS motif; however, this motif is only found when the N-terminal hinge contains tryptophan. | ||
</StructureSection> | </StructureSection> | ||
== 3D Structures of triose phosphate isomerase== | == 3D Structures of triose phosphate isomerase== | ||