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3pcb
From Proteopedia
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|PDB= 3pcb |SIZE=350|CAPTION= <scene name='initialview01'>3pcb</scene>, resolution 2.19Å | |PDB= 3pcb |SIZE=350|CAPTION= <scene name='initialview01'>3pcb</scene>, resolution 2.19Å | ||
|SITE= <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> | |SITE= <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> | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=3HB:3-HYDROXYBENZOIC+ACID'>3HB</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3pcb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pcb OCA], [http://www.ebi.ac.uk/pdbsum/3pcb PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3pcb RCSB]</span> | ||
}} | }} | ||
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[[Category: Ohlendorf, D H.]] | [[Category: Ohlendorf, D H.]] | ||
[[Category: Orville, A M.]] | [[Category: Orville, A M.]] | ||
| - | [[Category: 3HB]] | ||
| - | [[Category: BME]] | ||
| - | [[Category: FE]] | ||
[[Category: dioxygenase]] | [[Category: dioxygenase]] | ||
[[Category: iron]] | [[Category: iron]] | ||
| Line 36: | Line 36: | ||
[[Category: oxidoreductase]] | [[Category: oxidoreductase]] | ||
| - | ''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 05:35:08 2008'' |
Revision as of 02:35, 31 March 2008
| |||||||
| , resolution 2.19Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , , , , , , , , , and | ||||||
| Ligands: | , , | ||||||
| Activity: | Protocatechuate 3,4-dioxygenase, with EC number 1.13.11.3 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. 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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