1q0c: Difference between revisions

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-[[Image:1q0c.jpg|left|200px]]
- {{Structure
+==Anerobic Substrate Complex of Homoprotocatechuate 2,3-Dioxygenase from Brevibacterium fuscum. (Complex with 3,4-Dihydroxyphenylacetate)==
-|PDB= 1q0c |SIZE=350|CAPTION= <scene name='initialview01'>1q0c</scene>, resolution 2.1&Aring;
+<StructureSection load='1q0c' size='340' side='right'caption='[[1q0c]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=DHY:2-(3,4-DIHYDROXYPHENYL)ACETIC+ACID'>DHY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>
+<table><tr><td colspan='2'>[[1q0c]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevibacterium_fuscum Brevibacterium fuscum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q0C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q0C FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/3,4-dihydroxyphenylacetate_2,3-dioxygenase 3,4-dihydroxyphenylacetate 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.15 1.13.11.15] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DHY:2-(3,4-DIHYDROXYPHENYL)ACETIC+ACID'>DHY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1q0c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q0c OCA], [https://pdbe.org/1q0c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q0c RCSB], [https://www.ebi.ac.uk/pdbsum/1q0c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q0c ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1f1x|1F1X]], [[1f1y|1F1Y]], [[1f1r|1F1R]], [[1f1u|1F1U]], [[1f1v|1F1V]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q0c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q0c OCA], [http://www.ebi.ac.uk/pdbsum/1q0c PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1q0c RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/Q45135_9MICO Q45135_9MICO]
+== 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/q0/1q0c_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=1q0c ConSurf].
+<div style="clear:both"></div>
-'''Anerobic Substrate Complex of Homoprotocatechuate 2,3-Dioxygenase from Brevibacterium fuscum. (Complex with 3,4-Dihydroxyphenylacetate)'''
+==See Also==
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-The X-ray crystal structures of homoprotocatechuate 2,3-dioxygenases isolated from Arthrobacter globiformis and Brevibacterium fuscum have been determined to high resolution. These enzymes exhibit 83% sequence identity, yet their activities depend on different transition metals, Mn2+ and Fe2+, respectively. The structures allow the origins of metal ion selectivity and aspects of the molecular mechanism to be examined in detail. The homotetrameric enzymes belong to the type I family of extradiol dioxygenases (vicinal oxygen chelate superfamily); each monomer has four betaalphabetabetabeta modules forming two structurally homologous N-terminal and C-terminal barrel-shaped domains. The active-site metal is located in the C-terminal barrel and is ligated by two equatorial ligands, H214NE1 and E267OE1; one axial ligand, H155NE1; and two to three water molecules. The first and second coordination spheres of these enzymes are virtually identical (root mean square difference over all atoms, 0.19 A), suggesting that the metal selectivity must be due to changes at a significant distance from the metal and/or changes that occur during folding. The substrate (2,3-dihydroxyphenylacetate [HPCA]) chelates the metal asymmetrically at sites trans to the two imidazole ligands and interacts with a unique, mobile C-terminal loop. The loop closes over the bound substrate, presumably to seal the active site as the oxygen activation process commences. An "open" coordination site trans to E267 is the likely binding site for O2. The geometry of the enzyme-substrate complexes suggests that if a transiently formed metal-superoxide complex attacks the substrate without dissociation from the metal, it must do so at the C-3 position. Second-sphere active-site residues that are positioned to interact with the HPCA and/or bound O2 during catalysis are identified and discussed in the context of current mechanistic hypotheses.
-==About this Structure==
-Q0C is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Brevibacterium_fuscum Brevibacterium fuscum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q0C OCA].
-==Reference==
-Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases., Vetting MW, Wackett LP, Que L Jr, Lipscomb JD, Ohlendorf DH, J Bacteriol. 2004 Apr;186(7):1945-58. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15028678 15028678]
-[[Category: 3,4-dihydroxyphenylacetate 2,3-dioxygenase]]
 [[Category: Brevibacterium fuscum]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Lipscomb, J D.]]
+[[Category: Lipscomb JD]]
-[[Category: Ohlendorf, D H.]]
+[[Category: Ohlendorf DH]]
-[[Category: Que, L.]]
+[[Category: Que L]]
-[[Category: Vetting, M W.]]
+[[Category: Vetting MW]]
-[[Category: Wackett, L P.]]
+[[Category: Wackett LP]]
-[[Category: extradiol dioxygenase]]
-[[Category: substrate complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:07:06 2008''