2d80
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 2d80 |SIZE=350|CAPTION= <scene name='initialview01'>2d80</scene>, resolution 1.70Å | |PDB= 2d80 |SIZE=350|CAPTION= <scene name='initialview01'>2d80</scene>, resolution 1.70Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2d81|2D81]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d80 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d80 OCA], [http://www.ebi.ac.uk/pdbsum/2d80 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2d80 RCSB]</span> | ||
}} | }} | ||
| Line 31: | Line 34: | ||
[[Category: circular permutation]] | [[Category: circular permutation]] | ||
| - | ''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 02:31:11 2008'' |
Revision as of 23:31, 30 March 2008
| |||||||
| , resolution 1.70Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Activity: | Poly(3-hydroxybutyrate) depolymerase, with EC number 3.1.1.75 | ||||||
| Related: | 2D81
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of PHB depolymerase from Penicillium funiculosum
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
2D80 is a Single protein structure of sequence 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
Page seeded by OCA on Mon Mar 31 02:31:11 2008
