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| | ==STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3,4-DIHYDROXYPHENYLACETATE== | | ==STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3,4-DIHYDROXYPHENYLACETATE== |
| - | <StructureSection load='3pcn' size='340' side='right' caption='[[3pcn]], [[Resolution|resolution]] 2.40Å' scene=''> | + | <StructureSection load='3pcn' size='340' side='right'caption='[[3pcn]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3pcn]] is a 12 chain structure with sequence 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=3PCN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PCN FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3pcn]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PCN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PCN FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=DHY:2-(3,4-DIHYDROXYPHENYL)ACETIC+ACID'>DHY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=DHY:2-(3,4-DIHYDROXYPHENYL)ACETIC+ACID'>DHY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3pcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pcn OCA], [http://pdbe.org/3pcn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pcn RCSB], [http://www.ebi.ac.uk/pdbsum/3pcn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pcn ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pcn OCA], [https://pdbe.org/3pcn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pcn RCSB], [https://www.ebi.ac.uk/pdbsum/3pcn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pcn ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PCXA_PSEPU PCXA_PSEPU]] Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway. [[http://www.uniprot.org/uniprot/PCXB_PSEPU PCXB_PSEPU]] Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway. | + | [https://www.uniprot.org/uniprot/PCXA_PSEPU PCXA_PSEPU] Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Dioxygenase|Dioxygenase]] | + | *[[Dioxygenase 3D structures|Dioxygenase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Protocatechuate 3,4-dioxygenase]] | + | [[Category: Large Structures]] |
| | [[Category: Pseudomonas putida]] | | [[Category: Pseudomonas putida]] |
| - | [[Category: Lipscomb, J D]] | + | [[Category: Lipscomb JD]] |
| - | [[Category: Ohlendorf, D H]] | + | [[Category: Ohlendorf DH]] |
| - | [[Category: Orville, A M]] | + | [[Category: Orville AM]] |
| - | [[Category: Dioxygenase]]
| + | |
| - | [[Category: Iron]]
| + | |
| - | [[Category: Metalloprotein]]
| + | |
| - | [[Category: Nonheme]]
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| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Substrate complex]]
| + | |
| Structural highlights
Function
PCXA_PSEPU Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The crystal structure of the anaerobic complex of Pseudomonas putida protocatechuate 3,4-dioxygenase (3,4-PCD) bound with the alternative substrate, 3,4-dihydroxyphenylacetate (HPCA), is reported at 2.4 A resolution and refined to an R factor of 0.17. Formation of the active site Fe(III).HPCA chelated complex causes the endogenous axial tyrosinate, Tyr447 (147beta), to dissociate from the iron and rotate into an alternative orientation analogous to that previously observed in the anaerobic 3,4-PCD.3,4-dihydroxybenzoate complex (3, 4-PCD.PCA) [Orville, A. M., Lipscomb, J. D., & Ohlendorf, D. H. (1997) Biochemistry 36, 10052-10066]. Two orientations of the aromatic ring of HPCA related by an approximate 180 degrees rotation within the active site are consistent with the electron density. Resonance Raman (rR) spectroscopic data from Brevibacteriumfuscum 3,4-PCD.HPCA complex in solution reveals low frequency rR vibrational bands between 500 and 650 cm-1 as well as a band at approximately 1320 cm-1 which are diagnostic of a HPCA. Fe(III) chelate complex. 18O labeling of HPCA at either the C4 or C3 hydroxyl group unambiguously establishes the vibrational coupling modes associated with the five-membered chelate ring system. Analysis of these data suggests that the Fe(III)-HPCAO4 bond is shorter than the Fe(III)-HPCAO3 bond. This consequently favors the model for the crystal structure in which the C3 phenolic function occupies the Fe3+ ligand site opposite the endogenous ligand Tyr408(Oeta) (108beta). This is essentially the same binding orientation as proposed for PCA in the crystal structure of the anaerobic 3,4-PCD.PCA complex based solely on direct modeling of the 2Fo - Fc electron density and suggests that this is the conformation required for catalysis.
Crystal structure and resonance Raman studies of protocatechuate 3,4-dioxygenase complexed with 3,4-dihydroxyphenylacetate.,Elgren TE, Orville AM, Kelly KA, Lipscomb JD, Ohlendorf DH, Que L Jr Biochemistry. 1997 Sep 23;36(38):11504-13. PMID:9298971[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Elgren TE, Orville AM, Kelly KA, Lipscomb JD, Ohlendorf DH, Que L Jr. Crystal structure and resonance Raman studies of protocatechuate 3,4-dioxygenase complexed with 3,4-dihydroxyphenylacetate. Biochemistry. 1997 Sep 23;36(38):11504-13. PMID:9298971 doi:10.1021/bi970691k
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