3pcb
From Proteopedia
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| - | [[Image:3pcb.jpg|left|200px]]<br /><applet load="3pcb" size=" | + | [[Image:3pcb.jpg|left|200px]]<br /><applet load="3pcb" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="3pcb, resolution 2.19Å" /> | caption="3pcb, resolution 2.19Å" /> | ||
'''STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYBENZOATE'''<br /> | '''STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYBENZOATE'''<br /> | ||
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==About this Structure== | ==About this Structure== | ||
| - | 3PCB is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida] with FE, BME and 3HB as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Protocatechuate_3,4-dioxygenase Protocatechuate 3,4-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.3 1.13.11.3] Known structural/functional Sites: <scene name='pdbsite=ACA:Site Aca Is The Active Site Of Protomer Consisting Of Ch ...'>ACA</scene>, <scene name='pdbsite=ACB:Site Acb Is The Active Site Of Protomer Consisting Of Ch ...'>ACB</scene>, <scene name='pdbsite=ACC:Site Acc Is The Active Site Of Protomer Consisting Of Ch ...'>ACC</scene>, <scene name='pdbsite=ACD:Site Acd Is The Active Site Of Protomer Consisting Of Ch ...'>ACD</scene>, <scene name='pdbsite=ACE:Site Ace Is The Active Site Of Protomer Consisting Of Ch ...'>ACE</scene>, <scene name='pdbsite=ACF:Site Acf Is The Active Site Of Protomer Consisting Of Ch ...'>ACF</scene>, <scene name='pdbsite=VEA:Site Vea Is The Vestigial Site Of Protomer Consisting Of ...'>VEA</scene>, <scene name='pdbsite=VEB:Site Veb Is The Vestigial Site Of Protomer Consisting Of ...'>VEB</scene>, <scene name='pdbsite=VEC:Site Vec Is The Vestigial Site Of Protomer Consisting Of ...'>VEC</scene>, <scene name='pdbsite=VED:Site Ved Is The Vestigial Site Of Protomer Consisting Of ...'>VED</scene>, <scene name='pdbsite=VEE:Site Vee Is The Vestigial Site Of Protomer Consisting Of ...'>VEE</scene> and <scene name='pdbsite=VEF:Site Vef Is The Vestigial Site Of Protomer Consisting Of ...'>VEF</scene>. Full crystallographic information is available from [http:// | + | 3PCB is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida] with <scene name='pdbligand=FE:'>FE</scene>, <scene name='pdbligand=BME:'>BME</scene> and <scene name='pdbligand=3HB:'>3HB</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Protocatechuate_3,4-dioxygenase Protocatechuate 3,4-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.3 1.13.11.3] Known structural/functional Sites: <scene name='pdbsite=ACA:Site+Aca+Is+The+Active+Site+Of+Protomer+Consisting+Of+Ch+...'>ACA</scene>, <scene name='pdbsite=ACB:Site+Acb+Is+The+Active+Site+Of+Protomer+Consisting+Of+Ch+...'>ACB</scene>, <scene name='pdbsite=ACC:Site+Acc+Is+The+Active+Site+Of+Protomer+Consisting+Of+Ch+...'>ACC</scene>, <scene name='pdbsite=ACD:Site+Acd+Is+The+Active+Site+Of+Protomer+Consisting+Of+Ch+...'>ACD</scene>, <scene name='pdbsite=ACE:Site+Ace+Is+The+Active+Site+Of+Protomer+Consisting+Of+Ch+...'>ACE</scene>, <scene name='pdbsite=ACF:Site+Acf+Is+The+Active+Site+Of+Protomer+Consisting+Of+Ch+...'>ACF</scene>, <scene name='pdbsite=VEA:Site+Vea+Is+The+Vestigial+Site+Of+Protomer+Consisting+Of+...'>VEA</scene>, <scene name='pdbsite=VEB:Site+Veb+Is+The+Vestigial+Site+Of+Protomer+Consisting+Of+...'>VEB</scene>, <scene name='pdbsite=VEC:Site+Vec+Is+The+Vestigial+Site+Of+Protomer+Consisting+Of+...'>VEC</scene>, <scene name='pdbsite=VED:Site+Ved+Is+The+Vestigial+Site+Of+Protomer+Consisting+Of+...'>VED</scene>, <scene name='pdbsite=VEE:Site+Vee+Is+The+Vestigial+Site+Of+Protomer+Consisting+Of+...'>VEE</scene> and <scene name='pdbsite=VEF:Site+Vef+Is+The+Vestigial+Site+Of+Protomer+Consisting+Of+...'>VEF</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PCB OCA]. |
==Reference== | ==Reference== | ||
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[[Category: oxidoreductase]] | [[Category: oxidoreductase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 10:52:11 2008'' |
Revision as of 08:52, 3 February 2008
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STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYBENZOATE
Overview
Protocatechuate 3,4-dioxygenase (3,4-PCD) catalyzes the oxidative ring, cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis, cis-muconate. Crystal structures of Pseudomonas putida3,4-PCD [quaternary, structure of (alphabetaFe3+)12] complexed with seven competitive, inhibitors [3-hydroxyphenylacetate (MHP), 4-hydroxyphenylacetate (PHP), 3-hydroxybenzoate (MHB), 4-hydroxybenzoate (PHB), 3-fluoro-4-hydroxybenzoate (FHB), 3-chloro-4-hydroxybenzoate (CHB), and, 3-iodo-4-hydroxybenzoate (IHB)] are reported at 2.0-2.2 A resolution with, R-factors of 0. 0.159-0.179. The inhibitors bind in a narrow active site, crevasse lined with residues that provide a microenvironment that closely, matches the chemical characteristics of the inhibitors. This results in as, little as 20% solvent-exposed surface area for the higher-affinity, inhibitors (PHB, CHB, and FHB). In uncomplexed 3,4-PCD, the active site, Fe3+ is bound at the bottom of the active site crevasse by four endogenous, ligands and a solvent molecule (Wat827). The orientations of the, endogenous ligands are relatively unperturbed in each inhibitor complex, but the inhibitors themselves bind to or near the iron in a range of, positions, all of which perturb the position of Wat827. The three, lowest-affinity inhibitors (MHP, PHP, and IHB) yield distorted trigonal, bipyramidal iron coordination geometry in which the inhibitor C4-phenolate, group displaces the solvent ligand. MHB binds within the active site, but, neither its C3-OH group nor the solvent molecule binds to the iron. The, C4-phenolate group of the three highest-affinity inhibitors (PHB, CHB, and, FHB) coordinates the Fe3+ adjacent to Wat827, resulting in a shift in its, position to yield a six-coordinate distorted octahedral geometry. The, range of inhibitor orientations may mimic the mechanistically significant, stages of substrate binding to 3, 4-PCD. The structure of the final, substrate complex is reported in the following paper [Orville, A. M., Lipscomb, J. D., & Ohlendorf, D. H. (1997) Biochemistry 36, 10052-10066].
About this Structure
3PCB is a Protein complex structure of sequences from Pseudomonas putida with , and as ligands. Active as Protocatechuate 3,4-dioxygenase, with EC number 1.13.11.3 Known structural/functional Sites: , , , , , , , , , , and . Full crystallographic information is available from OCA.
Reference
Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site., Orville AM, Elango N, Lipscomb JD, Ohlendorf DH, Biochemistry. 1997 Aug 19;36(33):10039-51. PMID:9254599
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