2q2n: Difference between revisions

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-{{Seed}}
-[[Image:2q2n.png|left|200px]]
-<!--
+==Crystal structure of Bacillus subtilis ferrochelatase in complex with deuteroporphyrin IX 2,4-disulfonic acid dihydrochloride==
-The line below this paragraph, containing "STRUCTURE_2q2n", creates the "Structure Box" on the page.
+<StructureSection load='2q2n' size='340' side='right'caption='[[2q2n]], [[Resolution|resolution]] 1.80&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'>[[2q2n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q2N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q2N 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]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H01:PROTOPORPHYRIN+IX+2,4-DISULFONIC+ACID'>H01</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_2q2n|  PDB=2q2n  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q2n OCA], [https://pdbe.org/2q2n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q2n RCSB], [https://www.ebi.ac.uk/pdbsum/2q2n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q2n ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CPFC_BACSU CPFC_BACSU] Involved in coproporphyrin-dependent heme b biosynthesis (PubMed:25646457, PubMed:25908396). Catalyzes the insertion of ferrous iron into coproporphyrin III to form Fe-coproporphyrin III (PubMed:25646457, PubMed:25908396). It can also insert iron into protoporphyrin IX (PubMed:1459957, PubMed:8119288, PubMed:21052751, PubMed:25646457). Has weaker activity with 2,4 disulfonate, deuteroporphyrin and 2,4 hydroxyethyl (PubMed:25646457, PubMed:12761666). In vitro, can also use Zn(2+) or Cu(2+) (PubMed:8119288, PubMed:16140324, PubMed:21052751, PubMed:12761666).<ref>PMID:12761666</ref> <ref>PMID:1459957</ref> <ref>PMID:16140324</ref> <ref>PMID:21052751</ref> <ref>PMID:25646457</ref> <ref>PMID:25826316</ref> <ref>PMID:25908396</ref> <ref>PMID:8119288</ref>
+== 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/q2/2q2n_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=2q2n ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The specific insertion of a divalent metal ion into tetrapyrrole macrocycles is catalyzed by a group of enzymes called chelatases. Distortion of the tetrapyrrole has been proposed to be an important component of the mechanism of metallation. We present the structures of two different inhibitor complexes: (1) N-methylmesoporphyrin (N-MeMP) with the His183Ala variant of Bacillus subtilis ferrochelatase; (2) the wild-type form of the same enzyme with deuteroporphyrin IX 2,4-disulfonic acid dihydrochloride (dSDP). Analysis of the structures showed that only one N-MeMP isomer out of the eight possible was bound to the protein and it was different from the isomer that was earlier found to bind to the wild-type enzyme. A comparison of the distortion of this porphyrin with other porphyrin complexes of ferrochelatase and a catalytic antibody with ferrochelatase activity using normal-coordinate structural decomposition reveals that certain types of distortion are predominant in all these complexes. On the other hand, dSDP, which binds closer to the protein surface compared to N-MeMP, does not undergo any distortion upon binding to the protein, underscoring that the position of the porphyrin within the active site pocket is crucial for generating the distortion required for metal insertion. In addition, in contrast to the wild-type enzyme, Cu(2+)-soaking of the His183Ala variant complex did not show any traces of porphyrin metallation. Collectively, these results provide new insights into the role of the active site residues of ferrochelatase in controlling stereospecificity, distortion and metallation.
-===Crystal structure of Bacillus subtilis ferrochelatase in complex with deuteroporphyrin IX 2,4-disulfonic acid dihydrochloride===
+Porphyrin binding and distortion and substrate specificity in the ferrochelatase reaction: the role of active site residues.,Karlberg T, Hansson MD, Yengo RK, Johansson R, Thorvaldsen HO, Ferreira GC, Hansson M, Al-Karadaghi S J Mol Biol. 2008 May 16;378(5):1074-83. Epub 2008 Mar 28. PMID:18423489<ref>PMID:18423489</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2q2n" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18423489}}, adds the Publication Abstract to the page
+*[[Ferrochelatase 3D structures|Ferrochelatase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18423489 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18423489}}
+__TOC__
+</StructureSection>
-==About this Structure==
-Q2N is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q2N OCA].
-==Reference==
-Porphyrin binding and distortion and substrate specificity in the ferrochelatase reaction: the role of active site residues., Karlberg T, Hansson MD, Yengo RK, Johansson R, Thorvaldsen HO, Ferreira GC, Hansson M, Al-Karadaghi S, J Mol Biol. 2008 May 16;378(5):1074-83. Epub 2008 Mar 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18423489 18423489]
 [[Category: Bacillus subtilis]]
-[[Category: Ferrochelatase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Al-Karadaghi S]]
-[[Category: Al-Karadaghi, S.]]
+[[Category: Karlberg T]]
-[[Category: Karlberg, T.]]
+[[Category: Thorvaldsen OH]]
-[[Category: Thorvaldsen, O H.]]
-[[Category: Pi-helix]]
-[[Category: Rossman fold]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 23 10:06:52 2008''