Garman lab: Interconversion of lysosomal enzyme specificities: Difference between revisions
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==How this page was created== | ==How this page was created== | ||
The goal of this page is to provide three-dimensional and interactive figures to explore the structures determined for the 2010 paper "Interconversion of the Specificities of Human Lysosomal Enzymes Associated with Fabry and Schindler Diseases" by Ivan B. Tomasic, Matthew C. Metcalf, Abigail I. Guce, Nathaniel E. Clark and Scott C. Garman<ref name=primary>DOI: 10.1074/jbc.M110.118588</ref>. The starting point are the figures found in this paper. Biochemistry students at Westfield State University recreated these figures in jmol, and revised them after getting feedback from the authors. A special thank you goes to Susan Al Mahrwuth, Samuel J. Butler, Susy Civil, Westin G. Cohen, Allison F. DeVivo, Tyler S. Fassett, Courtney M. Fisher, Kimberly Garcia, Stephanie L. Hardy, Maureen W. Kamau, Sienna R. Kardel, Allyson L. Kress, Julia M. Lahaie, Stephen A. Malerba, Brittany E. Ricci, Kimberly Rosario, Yelena Vynar, and Deanna N. Womack for creating the initial figures and captions. If you are interested to learn how these figures were made, take a look at the discussion page (2nd tab above). | The goal of this page is to provide three-dimensional and interactive figures to explore the structures determined for the 2010 paper "Interconversion of the Specificities of Human Lysosomal Enzymes Associated with Fabry and Schindler Diseases" by Ivan B. Tomasic, Matthew C. Metcalf, Abigail I. Guce, Nathaniel E. Clark and Scott C. Garman<ref name=primary>DOI: 10.1074/jbc.M110.118588</ref>. The starting point are the figures found in this paper. Biochemistry students at Westfield State University recreated these figures in jmol, and revised them after getting feedback from the authors. A special thank you goes to Susan Al Mahrwuth, Samuel J. Butler, Susy Civil, Westin G. Cohen, Allison F. DeVivo, Tyler S. Fassett, Courtney M. Fisher, Kimberly Garcia, Stephanie L. Hardy, Maureen W. Kamau, Sienna R. Kardel, Allyson L. Kress, Julia M. Lahaie, Stephen A. Malerba, Brittany E. Ricci, Kimberly Rosario, Yelena Vynar, and Deanna N. Womack for creating the initial figures and captions. If you are interested to learn how these figures were made, take a look at the discussion page ([http://proteopedia.org/wiki/index.php/Talk:Garman_lab:_Interconversion_of_lysosomal_enzyme_specificities 2nd tab above]). | ||
== Lysosomal storage disease == | == Lysosomal storage disease == | ||
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The researchers asked the following question: Is it possible to turn one enzyme into the other (in terms of reaction catalyzed)? Their hypothesis was that a simple swap of the two amino acids in the active site that are different would accomplish an interconversion of specificities. | The researchers asked the following question: Is it possible to turn one enzyme into the other (in terms of reaction catalyzed)? Their hypothesis was that a simple swap of the two amino acids in the active site that are different would accomplish an interconversion of specificities. | ||
To test this, they made variants called GAL(SA) and NAGAL(EL), in which one active site has the amino acids of the other active site and vice versa (by swapping the two residues that are different). The data obtained by enzyme kinetics supported their hypothesis; the preference for galactose vs N-acetyl galactosamine is swapped (not shown here, but the data is in their paper<ref name=primary/>). Crystal structures (Fig. 2 panel A and B) show how GAL(SA) is able to bind to either <scene name='78/786673/Fig2a_galnac_complex/2'>N-acetyl galactosamine</scene> or <scene name='78/786673/Galsa_gal/21'>galactose</scene>. Comparing the structures of the NAGAL: N-acetyl galactosamine complex and the GAL(SA): N-acetyl galactosamine complex (Fig. 2 panel D) shows that <scene name='78/786673/ | To test this, they made variants called GAL(SA) and NAGAL(EL), in which one active site has the amino acids of the other active site and vice versa (by swapping the two residues that are different). The data obtained by enzyme kinetics supported their hypothesis; the preference for galactose vs N-acetyl galactosamine is swapped (not shown here, but the data is in their paper<ref name=primary/>). Crystal structures (Fig. 2 panel A and B) show how GAL(SA) is able to bind to either <scene name='78/786673/Fig2a_galnac_complex/2'>N-acetyl galactosamine</scene> or <scene name='78/786673/Galsa_gal/21'>galactose</scene>. Comparing the structures of the NAGAL: N-acetyl galactosamine complex and the GAL(SA): N-acetyl galactosamine complex (Fig. 2 panel D) shows that <scene name='78/786673/Nagal_galsa_superposition/1'>they bind the ligand in a very similar manner</scene>. | ||
You can explore the structural data further by going through the figures below and clicking on the buttons. If during your exploration you get lost or some figures behave strangely, press <scene name='78/786673/Galnac/2'>here</scene> first to reset the 3D browser and then try again. | You can explore the structural data further by going through the figures below and clicking on the buttons. If during your exploration you get lost or some figures behave strangely, press <scene name='78/786673/Galnac/2'>here</scene> first to reset the 3D browser and then try again. | ||
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<jmol> | <jmol> | ||
<jmolButton> | <jmolButton> | ||
<script>!exit; ppdiaCaptionCmd = "changeCaption('The enyme GAL (green) in complex with the sugar galactose. ','white','black');"; javascript @ppdiaCaptionCmd | <script>!exit; ppdiaCaptionCmd = "changeCaption('The enyme GAL (green) in complex with the sugar galactose. ','white','black');"; javascript @ppdiaCaptionCmd; model 1</script> | ||
<text>GAL</text> | <text>GAL</text> | ||
</jmolButton> | </jmolButton> | ||
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<jmolButton> | <jmolButton> | ||
<script>!exit; ppdiaCaptionCmd = "changeCaption('The enyme NAGAL (blue) in complex with the sugar N-acetyl galactosamin. ','white','black');"; | <script>!exit; ppdiaCaptionCmd = "changeCaption('The enyme NAGAL (blue) in complex with the sugar N-acetyl galactosamin. ','white','black');"; | ||
javascript @ppdiaCaptionCmd | javascript @ppdiaCaptionCmd;model 2</script> | ||
<text>NAGAL</text> | <text>NAGAL</text> | ||
</jmolButton> | </jmolButton> | ||
</jmol> <jmol> | </jmol> <jmol> | ||
<jmolButton> | <jmolButton> | ||
<script>!exit; ppdiaCaptionCmd = "changeCaption('Superposition of GAL (green) and NAGAL (blue).','white','black');"; javascript @ppdiaCaptionCmd | <script>!exit; ppdiaCaptionCmd = "changeCaption('Superposition of GAL (green) and NAGAL (blue).','white','black');"; javascript @ppdiaCaptionCmd; model 0</script> | ||
<text>both</text> | <text>both</text> | ||
</jmolButton> | </jmolButton> | ||
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GAL(SA) is derived from GAL by replacing actives site residues glutamate 203 with serine and leucine 206 with alanine. Having these smaller amino acids in the active site increases the substrate binding cavity, and makes the active site of αGAL(SA) very similar to that of αNAGAL. With these substitutions, the catalytic activity of GAL(SA) is more similar to NAGAL than to GAL (the data is not shown here, but can be found in the research paper<ref name=primary/>). | GAL(SA) is derived from GAL by replacing actives site residues glutamate 203 with serine and leucine 206 with alanine. Having these smaller amino acids in the active site increases the substrate binding cavity, and makes the active site of αGAL(SA) very similar to that of αNAGAL. With these substitutions, the catalytic activity of GAL(SA) is more similar to NAGAL than to GAL (the data is not shown here, but can be found in the research paper<ref name=primary/>). | ||
<jmol><jmolLink><script>script "/scripts/78/786673/Fig2a_galnac_complex/ | <jmol><jmolLink><script>script "/scripts/78/786673/Fig2a_galnac_complex/3.spt"; ppdiaCaptionCmd = "changeCaption('Crystal structure of GAL(SA) bound to N-acetyl galactosamine. GAL(SA) active site residues are shown in yellow and the product, N-acetyl galactosamine, is shown in gray. The blue mesh around the sugar represents its (2Fo-Fc) electron density.','white','black');";javascript @ppdiaCaptionCmd;model 2; model 2</script><text>Panel A</text></jmolLink></jmol>: in complex with N-acetyl galactosamine | ||
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</jmol> | </jmol> | ||
<jmol><jmolLink><script>script "/scripts/78/786673/Galsa_gal/ | <jmol><jmolLink><script>script "/scripts/78/786673/Galsa_gal/2.spt"; ppdiaCaptionCmd = "changeCaption('Crystal structure of GAL(SA) bound to galactose. GAL(SA) active site residues are shown in yellow and the product, galactose, is shown in gray. The blue mesh around the sugar represents its (2Fo-Fc) electron density.','white','black');";javascript @ppdiaCaptionCmd;model 2; model 2</script><text>Panel B</text></jmolLink></jmol>: in complex with galactose | ||
<jmol> | <jmol> | ||
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</jmolButton> | </jmolButton> | ||
</jmol> | </jmol> | ||
<scene name='78/786673/Nagal_galsa_superposition/1'>Panel D</scene>: Superposition with alpha-NAGAL bound to GalNAc | <scene name='78/786673/Nagal_galsa_superposition/1'>Panel D</scene>: Superposition with alpha-NAGAL bound to GalNAc | ||