3bf8: Difference between revisions
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'''1.1 resolution structure of ybfF, a new esterase from Escherichia coli: a unique substrate-binding crevice generated by domain arrangement''' | {{Structure | ||
|PDB= 3bf8 |SIZE=350|CAPTION= <scene name='initialview01'>3bf8</scene>, resolution 1.68Å | |||
|SITE= <scene name='pdbsite=AC1:Mla+Binding+Site+For+Residue+A+4892'>AC1</scene> and <scene name='pdbsite=AC2:Mla+Binding+Site+For+Residue+B+4892'>AC2</scene> | |||
|LIGAND= <scene name='pdbligand=MLA:MALONIC ACID'>MLA</scene> | |||
|ACTIVITY= | |||
|GENE= K12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |||
}} | |||
'''1.1 resolution structure of ybfF, a new esterase from Escherichia coli: a unique substrate-binding crevice generated by domain arrangement''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
3BF8 is a [ | 3BF8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BF8 OCA]. | ||
==Reference== | ==Reference== | ||
High-resolution structure of ybfF from Escherichia coli K12: a unique substrate-binding crevice generated by domain arrangement., Park SY, Lee SH, Lee J, Nishi K, Kim YS, Jung CH, Kim JS, J Mol Biol. 2008 Mar 7;376(5):1426-37. Epub 2008 Jan 4. PMID:[http:// | High-resolution structure of ybfF from Escherichia coli K12: a unique substrate-binding crevice generated by domain arrangement., Park SY, Lee SH, Lee J, Nishi K, Kim YS, Jung CH, Kim JS, J Mol Biol. 2008 Mar 7;376(5):1426-37. Epub 2008 Jan 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18215690 18215690] | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: ybff]] | [[Category: ybff]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:58:27 2008'' | ||
Revision as of 19:58, 20 March 2008
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| , resolution 1.68Å | |||||||
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| Sites: | and | ||||||
| Ligands: | |||||||
| Gene: | K12 (Escherichia coli) | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
1.1 resolution structure of ybfF, a new esterase from Escherichia coli: a unique substrate-binding crevice generated by domain arrangement
OverviewOverview
Esterases are one of the most common enzymes and are involved in diverse cellular functions. ybfF protein from Escherichia coli (Ec_ybfF) belongs to the esterase family for the large substrates, palmitoyl coenzyme A and malonyl coenzyme A, which are important cellular intermediates for energy conversion and biomolecular synthesis. To obtain molecular information on ybfF esterase, which is found in a wide range of microorganisms, we elucidated the crystal structures of Ec_ybfF in complexes with small molecules at resolutions of 1.1 and 1.68 A, respectively. The structure of Ec_ybfF is composed of a globular alpha/beta hydrolase domain with a three-helical bundle cap, which is linked by a kinked helix to the alpha/beta hydrolase domain. It contains a catalytic tetrad of Ser-His-Asp-Ser with the first Ser acting as a nucleophile. The unique spatial arrangement and orientation of the helical cap with respect to the alpha/beta hydrolase domain form a substrate-binding crevice for large substrates. The helical cap is also directly involved in catalysis by providing a substrate anchor, viz., the conserved residues of Arg123 and Tyr208. The high-resolution structure of Ec_ybfF shows that the inserted helical bundle structure and its spatial orientation with respect to the alpha/beta hydrolase domain are critical for creating a large inner space and constituting a specific active site, thereby providing the broad substrate spectrum toward large biomolecules.
About this StructureAbout this Structure
3BF8 is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
ReferenceReference
High-resolution structure of ybfF from Escherichia coli K12: a unique substrate-binding crevice generated by domain arrangement., Park SY, Lee SH, Lee J, Nishi K, Kim YS, Jung CH, Kim JS, J Mol Biol. 2008 Mar 7;376(5):1426-37. Epub 2008 Jan 4. PMID:18215690
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