1xd1: Difference between revisions
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|PDB= 1xd1 |SIZE=350|CAPTION= <scene name='initialview01'>1xd1</scene>, resolution 2.2Å | |PDB= 1xd1 |SIZE=350|CAPTION= <scene name='initialview01'>1xd1</scene>, resolution 2.2Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=6SA:ACARBOSE+DERIVED+HEXASACCHARIDE'>6SA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span> | ||
|GENE= AMY2A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | |GENE= AMY2A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1xcw|1XCW]], [[1xcx|1XCX]], [[1xd0|1XD0]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xd1 OCA], [http://www.ebi.ac.uk/pdbsum/1xd1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xd1 RCSB]</span> | |||
}} | }} | ||
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[[Category: Park, K H.]] | [[Category: Park, K H.]] | ||
[[Category: Withers, S G.]] | [[Category: Withers, S G.]] | ||
[[Category: acarbose]] | [[Category: acarbose]] | ||
[[Category: acarbose analogue]] | [[Category: acarbose analogue]] | ||
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[[Category: structure]] | [[Category: structure]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:47:55 2008'' | ||
Revision as of 00:47, 31 March 2008
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| , resolution 2.2Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Gene: | AMY2A (Homo sapiens) | ||||||
| Activity: | Alpha-amylase, with EC number 3.2.1.1 | ||||||
| Related: | 1XCW, 1XCX, 1XD0
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Acarbose Rearrangement Mechanism Implied by the Kinetic and Structural Analysis of Human Pancreatic alpha-Amylase in Complex with Analogues and Their Elongated Counterparts
OverviewOverview
A mechanistic study of the poorly understood pathway by which the inhibitor acarbose is enzymatically rearranged by human pancreatic alpha-amylase has been conducted by structurally examining the binding modes of the related inhibitors isoacarbose and acarviosine-glucose, and by novel kinetic measurements of all three inhibitors under conditions that demonstrate this rearrangement process. Unlike acarbose, isoacarbose has a unique terminal alpha-(1-6) linkage to glucose and is found to be resistant to enzymatic rearrangement. This terminal glucose unit is found to bind in the +3 subsite and for the first time reveals the interactions that occur in this part of the active site cleft with certainty. These results also suggest that the +3 binding subsite may be sufficiently flexible to bind the alpha-(1-6) branch points in polysaccharide substrates, and therefore may play a role in allowing efficient cleavage in the direct vicinity of such junctures. Also found to be resistant to enzymatic rearrangement was acarviosine-glucose, which has one fewer glucose unit than acarbose. Collectively, structural studies of all three inhibitors and the specific cleavage pattern of HPA make it possible to outline the simplest sequence of enzymatic reactions likely involved upon acarbose binding. Prominent features incorporated into the starting structure of acarbose to facilitate the synthesis of the final tightly bound pseudo-pentasaccharide product are the restricted availability of hydrolyzable bonds and the placement of the transition state-like acarviosine group. Additional "in situ" experiments designed to elongate and thereby optimize isoacarbose and acarviosine-glucose inhibition using the activated substrate alphaG3F demonstrate the feasibility of this approach and that the principles outlined for acarbose rearrangement can be used to predict the final products that were obtained.
About this StructureAbout this Structure
1XD1 is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
ReferenceReference
Acarbose rearrangement mechanism implied by the kinetic and structural analysis of human pancreatic alpha-amylase in complex with analogues and their elongated counterparts., Li C, Begum A, Numao S, Park KH, Withers SG, Brayer GD, Biochemistry. 2005 Mar 8;44(9):3347-57. PMID:15736945
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