3pca
From Proteopedia
| Line 1: | Line 1: | ||
| - | [[Image:3pca.gif|left|200px]] | + | [[Image:3pca.gif|left|200px]] |
| - | + | ||
| - | '''STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3,4-DIHYDROXYBENZOATE''' | + | {{Structure |
| + | |PDB= 3pca |SIZE=350|CAPTION= <scene name='initialview01'>3pca</scene>, resolution 2.20Å | ||
| + | |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=S2M:Secondary+Three-Fold+Site+Between+M,+N,+O+Chains'>S2M</scene>, <scene name='pdbsite=S2P:Secondary+Three-Fold+Site+Between+P,+Q,+R+Chains'>S2P</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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene> and <scene name='pdbligand=DHB:3,4-DIHYDROXYBENZOIC ACID'>DHB</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] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3,4-DIHYDROXYBENZOATE''' | ||
| + | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | 3PCA is a [ | + | 3PCA is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PCA OCA]. |
==Reference== | ==Reference== | ||
| - | Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding., Orville AM, Lipscomb JD, Ohlendorf DH, Biochemistry. 1997 Aug 19;36(33):10052-66. PMID:[http:// | + | Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding., Orville AM, Lipscomb JD, Ohlendorf DH, Biochemistry. 1997 Aug 19;36(33):10052-66. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9254600 9254600] |
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Protocatechuate 3,4-dioxygenase]] | [[Category: Protocatechuate 3,4-dioxygenase]] | ||
| Line 27: | Line 36: | ||
[[Category: substrate complex]] | [[Category: substrate complex]] | ||
| - | ''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 19:06:19 2008'' |
Revision as of 17:06, 20 March 2008
| |||||||
| , resolution 2.20Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , , , , , , , , , , , and | ||||||
| Ligands: | , and | ||||||
| Activity: | Protocatechuate 3,4-dioxygenase, with EC number 1.13.11.3 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3,4-DIHYDROXYBENZOATE
Overview
Protocatechuate 3,4-dioxygenase (3,4-PCD) utilizes a ferric ion to catalyze the aromatic ring cleavage of 3,4-dihydroxybenzoate (PCA) by incorporation of both atoms of dioxygen to yield beta-carboxy-cis, cis-muconate. The crystal structures of the anaerobic 3,4-PCD.PCA complex, aerobic complexes with two heterocyclic PCA analogs, 2-hydroxyisonicotinic acid N-oxide (INO) and 6-hydroxynicotinic acid N-oxide (NNO), and ternary complexes of 3,4-PCD.INO.CN and 3,4-PCD. NNO.CN have been determined at 2.1-2.2 A resolution and refined to R-factors between 0.165 and 0.184. PCA, INO, and NNO form very similar, asymmetrically chelated complexes with the active site Fe3+ that result in dissociation of the endogenous axial tyrosinate Fe3+ ligand, Tyr447 (147beta). After its release from the iron, Tyr447 is stabilized by hydrogen bonding to Tyr16 (16alpha) and Asp413 (113beta) and forms the top of a small cavity adjacent to the C3-C4 bond of PCA. The equatorial Fe3+ coordination site within this cavity is unoccupied in the anaerobic 3,4-PCD.PCA complex but coordinates a solvent molecule in the 3,4-PCD.INO and 3,4-PCD.NNO complexes and CN- in the 3,4-PCD.INO.CN and 3,4-PCD.NNO.CN complexes. This shows that an O2 analog can occupy the cavity and suggests that electrophilic O2 attack on PCA is initiated from this site. Both the dissociation of the endogenous Tyr447 and the expansion of the iron coordination sphere are novel features of the 3,4-PCD. substrate complex which appear to play essential roles in the activation of substrate for O2 attack. Together, the structures presented here and in the preceding paper [Orville, A. M., Elango, N. , Lipscomb, J. D., & Ohlendorf, D. H. (1997) Biochemistry 36, 10039-10051] provide atomic models for several steps in the reaction cycle of 3,4-PCD and related Fe3+-containing dioxygenases.
About this Structure
3PCA is a Protein complex structure of sequences from Pseudomonas putida. Full crystallographic information is available from OCA.
Reference
Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding., Orville AM, Lipscomb JD, Ohlendorf DH, Biochemistry. 1997 Aug 19;36(33):10052-66. PMID:9254600
Page seeded by OCA on Thu Mar 20 19:06:19 2008
