3amk: Difference between revisions

<StructureSection load='3amk' size='340' side='right' caption='[[3amk]], [[Resolution|resolution]] 1.90&Aring;' scene=''>

<table><tr><td colspan='2'>[[3amk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AMK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AMK FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>

<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Os06g0726400, SBE1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3amk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3amk OCA], [http://pdbe.org/3amk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3amk RCSB], [http://www.ebi.ac.uk/pdbsum/3amk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3amk ProSAT]</span></td></tr>

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== Publication Abstract from PubMed ==

Starch-branching enzyme catalyzes the cleavage of alpha-1, 4-linkages and the subsequent transfer of alpha-1,4 glucan to form an alpha-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central alpha-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the alpha-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 A by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the alpha-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase.

 

Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.,Noguchi J, Chaen K, Vu NT, Akasaka T, Shimada H, Nakashima T, Nishi A, Satoh H, Omori T, Kakuta Y, Kimura M Glycobiology. 2011 Aug;21(8):1108-16. Epub 2011 Apr 14. PMID:21493662<ref>PMID:21493662</ref>

 

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>

[[Category: Japanese rice]]

[[Category: Chaen, K]]

[[Category: Kakuta, Y]]

[[Category: Kimura, M]]

[[Category: Noguchi, J]]

[[Category: Vu, N]]

[[Category: Transferase]]