3pcj: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3pcj.png|left|200px]]
-<!--
+==STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 2-HYDROXYISONICOTINIC ACID N-OXIDE==
-The line below this paragraph, containing "STRUCTURE_3pcj", creates the "Structure Box" on the page.
+<StructureSection load='3pcj' size='340' side='right'caption='[[3pcj]], [[Resolution|resolution]] 2.13&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3pcj]] 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=3PCJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PCJ FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.13&#8491;</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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=INO:2-HYDROXYISONICOTINIC+ACID+N-OXIDE'>INO</scene></td></tr>
-{{STRUCTURE_3pcj|  PDB=3pcj  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pcj OCA], [https://pdbe.org/3pcj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pcj RCSB], [https://www.ebi.ac.uk/pdbsum/3pcj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pcj ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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 ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pc/3pcj_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3pcj ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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., &amp; 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.
-===STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 2-HYDROXYISONICOTINIC ACID N-OXIDE===
+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<ref>PMID:9254600</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3pcj" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9254600}}, adds the Publication Abstract to the page
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9254600 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9254600}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-PCJ is a 12 chains 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=3PCJ OCA].
-==Reference==
-<ref group="xtra">PMID:9254600</ref><references group="xtra"/>
-[[Category: Protocatechuate 3,4-dioxygenase]]
 [[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]]
-[[Category: Oxidoreductase]]
-[[Category: Transition-state analog complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 11:25:57 2009''