Triose Phosphate Isomerase: Difference between revisions
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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/Conserved1/1'>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. Hence, the conservation pattern shown is correct for TPI.</ref>.) | TPI has a roughly 50% sequence conservation from bacteria to humans.<ref>PMID:8130194</ref> The <scene name='Triose_Phosphate_Isomerase/Conserved1/1'>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. | ||