2d81
From Proteopedia
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| - | [[Image:2d81.gif|left|200px]] | + | [[Image:2d81.gif|left|200px]] |
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| - | '''PHB depolymerase (S39A) complexed with R3HB trimer''' | + | {{Structure |
| + | |PDB= 2d81 |SIZE=350|CAPTION= <scene name='initialview01'>2d81</scene>, resolution 1.66Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene> and <scene name='pdbligand=RB3:(1R)-3-{[(1R)-3-METHOXY-1-METHYL-3-OXOPROPYL]OXY}-1-METHYL-3-OXOPROPYL (3R)-3-HYDROXYBUTANOATE'>RB3</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/Poly(3-hydroxybutyrate)_depolymerase Poly(3-hydroxybutyrate) depolymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.75 3.1.1.75] | ||
| + | |GENE= phaZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28572 Penicillium funiculosum]) | ||
| + | }} | ||
| + | |||
| + | '''PHB depolymerase (S39A) complexed with R3HB trimer''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2D81 is a [ | + | 2D81 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Penicillium_funiculosum Penicillium funiculosum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D81 OCA]. |
==Reference== | ==Reference== | ||
| - | The crystal structure of polyhydroxybutyrate depolymerase from Penicillium funiculosum provides insights into the recognition and degradation of biopolyesters., Hisano T, Kasuya K, Tezuka Y, Ishii N, Kobayashi T, Shiraki M, Oroudjev E, Hansma H, Iwata T, Doi Y, Saito T, Miki K, J Mol Biol. 2006 Mar 3;356(4):993-1004. Epub 2005 Dec 27. PMID:[http:// | + | The crystal structure of polyhydroxybutyrate depolymerase from Penicillium funiculosum provides insights into the recognition and degradation of biopolyesters., Hisano T, Kasuya K, Tezuka Y, Ishii N, Kobayashi T, Shiraki M, Oroudjev E, Hansma H, Iwata T, Doi Y, Saito T, Miki K, J Mol Biol. 2006 Mar 3;356(4):993-1004. Epub 2005 Dec 27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16405909 16405909] |
[[Category: Penicillium funiculosum]] | [[Category: Penicillium funiculosum]] | ||
[[Category: Poly(3-hydroxybutyrate) depolymerase]] | [[Category: Poly(3-hydroxybutyrate) depolymerase]] | ||
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[[Category: circular permutation]] | [[Category: circular permutation]] | ||
| - | ''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 16:24:06 2008'' |
Revision as of 14:24, 20 March 2008
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| , resolution 1.66Å | |||||||
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| Ligands: | and | ||||||
| Gene: | phaZ (Penicillium funiculosum) | ||||||
| Activity: | Poly(3-hydroxybutyrate) depolymerase, with EC number 3.1.1.75 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
PHB depolymerase (S39A) complexed with R3HB trimer
Overview
Polyhydroxybutyrate is a microbial polyester that can be produced from renewable resources, and is degraded by the enzyme polyhydroxybutyrate depolymerase. The crystal structures of polyhydroxybutyrate depolymerase from Penicillium funiculosum and its S39 A mutant complexed with the methyl ester of a trimer substrate of (R)-3-hydroxybutyrate have been determined at resolutions of 1.71 A and 1.66 A, respectively. The enzyme is comprised of a single domain, which represents a circularly permuted variant of the alpha/beta hydrolase fold. The catalytic residues Ser39, Asp121, and His155 are located at topologically conserved positions. The main chain amide groups of Ser40 and Cys250 form an oxyanion hole. A crevice is formed on the surface of the enzyme, to which a single polymer chain can be bound by predominantly hydrophobic interactions with several hydrophobic residues. The structure of the S39A mutant-trimeric substrate complex reveals that Trp307 is responsible for the recognition of the ester group adjacent to the scissile group. It is also revealed that the substrate-binding site includes at least three, and possibly four, subsites for binding monomer units of polyester substrates. Thirteen hydrophobic residues, which are exposed to solvent, are aligned around the mouth of the crevice, forming a putative adsorption site for the polymer surface. These residues may contribute to the sufficient binding affinity of the enzyme for PHB granules without a distinct substrate-binding domain.
About this Structure
2D81 is a Protein complex structure of sequences from Penicillium funiculosum. Full crystallographic information is available from OCA.
Reference
The crystal structure of polyhydroxybutyrate depolymerase from Penicillium funiculosum provides insights into the recognition and degradation of biopolyesters., Hisano T, Kasuya K, Tezuka Y, Ishii N, Kobayashi T, Shiraki M, Oroudjev E, Hansma H, Iwata T, Doi Y, Saito T, Miki K, J Mol Biol. 2006 Mar 3;356(4):993-1004. Epub 2005 Dec 27. PMID:16405909
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