2eae: Difference between revisions
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[[Image:2eae.gif|left|200px]] | [[Image:2eae.gif|left|200px]] | ||
'''Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complexes with products''' | {{Structure | ||
|PDB= 2eae |SIZE=350|CAPTION= <scene name='initialview01'>2eae</scene>, resolution 1.80Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=LAT:LACTOSE'>LAT</scene> and <scene name='pdbligand=CA:CALCIUM ION'>CA</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/1,2-alpha-L-fucosidase 1,2-alpha-L-fucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.63 3.2.1.63] | |||
|GENE= | |||
}} | |||
'''Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complexes with products''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2EAE is a [ | 2EAE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bifidobacterium_bifidum Bifidobacterium bifidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAE OCA]. | ||
==Reference== | ==Reference== | ||
Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum., Nagae M, Tsuchiya A, Katayama T, Yamamoto K, Wakatsuki S, Kato R, J Biol Chem. 2007 Jun 22;282(25):18497-509. Epub 2007 Apr 25. PMID:[http:// | Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum., Nagae M, Tsuchiya A, Katayama T, Yamamoto K, Wakatsuki S, Kato R, J Biol Chem. 2007 Jun 22;282(25):18497-509. Epub 2007 Apr 25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17459873 17459873] | ||
[[Category: 1,2-alpha-L-fucosidase]] | [[Category: 1,2-alpha-L-fucosidase]] | ||
[[Category: Bifidobacterium bifidum]] | [[Category: Bifidobacterium bifidum]] | ||
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[[Category: glycoside hydrolase]] | [[Category: glycoside hydrolase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:37:30 2008'' | ||
Revision as of 17:37, 20 March 2008
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| , resolution 1.80Å | |||||||
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| Ligands: | , , and | ||||||
| Activity: | 1,2-alpha-L-fucosidase, with EC number 3.2.1.63 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complexes with products
OverviewOverview
1,2-alpha-L-fucosidase (AfcA), which hydrolyzes the glycosidic linkage of Fucalpha1-2Gal via an inverting mechanism, was recently isolated from Bifidobacterium bifidum and classified as the first member of the novel glycoside hydrolase family 95. To better understand the molecular mechanism of this enzyme, we determined the x-ray crystal structures of the AfcA catalytic (Fuc) domain in unliganded and complexed forms with deoxyfuconojirimycin (inhibitor), 2'-fucosyllactose (substrate), and L-fucose and lactose (products) at 1.12-2.10 A resolution. The AfcA Fuc domain is composed of four regions, an N-terminal beta region, a helical linker, an (alpha/alpha)6 helical barrel domain, and a C-terminal beta region, and this arrangement is similar to bacterial phosphorylases. In the complex structures, the ligands were buried in the central cavity of the helical barrel domain. Structural analyses in combination with mutational experiments revealed that the highly conserved Glu566 probably acts as a general acid catalyst. However, no carboxylic acid residue is found at the appropriate position for a general base catalyst. Instead, a water molecule stabilized by Asn423 in the substrate-bound complex is suitably located to perform a nucleophilic attack on the C1 atom of L-fucose moiety in 2'-fucosyllactose, and its location is nearly identical near the O1 atom of beta-L-fucose in the products-bound complex. Based on these data, we propose and discuss a novel catalytic reaction mechanism of AfcA.
About this StructureAbout this Structure
2EAE is a Single protein structure of sequence from Bifidobacterium bifidum. Full crystallographic information is available from OCA.
ReferenceReference
Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum., Nagae M, Tsuchiya A, Katayama T, Yamamoto K, Wakatsuki S, Kato R, J Biol Chem. 2007 Jun 22;282(25):18497-509. Epub 2007 Apr 25. PMID:17459873
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