1ld3: Difference between revisions

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-{{Seed}}
-[[Image:1ld3.png|left|200px]]
-<!--
+==Crystal Structure of B. subilis ferrochelatase with Zn(2+) bound at the active site.==
-The line below this paragraph, containing "STRUCTURE_1ld3", creates the "Structure Box" on the page.
+<StructureSection load='1ld3' size='340' side='right'caption='[[1ld3]], [[Resolution|resolution]] 2.60&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'>[[1ld3]] 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=1LD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LD3 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]] 2.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1ld3|  PDB=1ld3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ld3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ld3 OCA], [https://pdbe.org/1ld3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ld3 RCSB], [https://www.ebi.ac.uk/pdbsum/1ld3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ld3 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/ld/1ld3_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=1ld3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ferrochelatase, the terminal enzyme in heme biosynthesis, catalyses metal insertion into protoporphyrin IX. The location of the metal binding site with respect to the bound porphyrin substrate and the mode of metal binding are of central importance for understanding the mechanism of porphyrin metallation. In this work we demonstrate that Zn(2+), which is commonly used as substrate in assays of the ferrochelatase reaction, and Cd(2+), an inhibitor of the enzyme, bind to the invariant amino acids His183 and Glu264 and water molecules, all located within the porphyrin binding cleft. On the other hand, Mg(2+), which has been shown to bind close to the surface at 7 A from His183, was largely absent from its site. Activity measurements demonstrate that Mg(2+) has a stimulatory effect on the enzyme, lowering K(M) for Zn(2+) from 55 to 24 micro M. Changing one of the Mg(2+) binding residues, Glu272, to serine abolishes the effect of Mg(2+). It is proposed that prior to metal insertion the metal may form a sitting-atop (SAT) complex with the invariant His-Glu couple and the porphyrin. Metal binding to the Mg(2+) site may stimulate metal release from the protein ligands and its insertion into the porphyrin.
-===Crystal Structure of B. subilis ferrochelatase with Zn(2+) bound at the active site.===
+Metal binding to Bacillus subtilis ferrochelatase and interaction between metal sites.,Lecerof D, Fodje MN, Alvarez Leon R, Olsson U, Hansson A, Sigfridsson E, Ryde U, Hansson M, Al-Karadaghi S J Biol Inorg Chem. 2003 Apr;8(4):452-8. Epub 2003 Jan 18. PMID:12761666<ref>PMID:12761666</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ld3" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12761666}}, adds the Publication Abstract to the page
+*[[Ferrochelatase 3D structures|Ferrochelatase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12761666 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12761666}}
+__TOC__
+</StructureSection>
-==About this Structure==
-LD3 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=1LD3 OCA].
-==Reference==
-Metal binding to Bacillus subtilis ferrochelatase and interaction between metal sites., Lecerof D, Fodje MN, Alvarez Leon R, Olsson U, Hansson A, Sigfridsson E, Ryde U, Hansson M, Al-Karadaghi S, J Biol Inorg Chem. 2003 Apr;8(4):452-8. Epub 2003 Jan 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12761666 12761666]
 [[Category: Bacillus subtilis]]
-[[Category: Ferrochelatase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Al-Karadaghi S]]
-[[Category: Al-Karadaghi, S.]]
+[[Category: Fodje MN]]
-[[Category: Fodje, M N.]]
+[[Category: Hansson A]]
-[[Category: Hansson, A.]]
+[[Category: Hansson M]]
-[[Category: Hansson, M.]]
+[[Category: Lecerof D]]
-[[Category: Lecerof, D.]]
+[[Category: Leon RA]]
-[[Category: Leon, R A.]]
+[[Category: Olsson U]]
-[[Category: Olsson, U.]]
+[[Category: Ryde U]]
-[[Category: Ryde, U.]]
+[[Category: Sigfridsson E]]
-[[Category: Sigfridsson, E.]]
-[[Category: Pi-helix]]
-[[Category: Rossmann fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  2 12:26:13 2008''