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1ld3

From Proteopedia

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Current revision

Crystal Structure of B. subilis ferrochelatase with Zn(2+) bound at the active site.

Structural highlights

1ld3 is a 1 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8]

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

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.

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^[9]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Lecerof D, Fodje MN, Alvarez Leon R, Olsson U, Hansson A, Sigfridsson E, Ryde U, Hansson M, Al-Karadaghi S. Metal binding to Bacillus subtilis ferrochelatase and interaction between metal sites. J Biol Inorg Chem. 2003 Apr;8(4):452-8. Epub 2003 Jan 18. PMID:12761666 doi:10.1007/s00775-002-0436-1
↑ Hansson M, Hederstedt L. Cloning and characterization of the Bacillus subtilis hemEHY gene cluster, which encodes protoheme IX biosynthetic enzymes. J Bacteriol. 1992 Dec;174(24):8081-93. PMID:1459957 doi:10.1128/jb.174.24.8081-8093.1992
↑ Shipovskov S, Karlberg T, Fodje M, Hansson MD, Ferreira GC, Hansson M, Reimann CT, Al-Karadaghi S. Metallation of the transition-state inhibitor N-methyl mesoporphyrin by ferrochelatase: implications for the catalytic reaction mechanism. J Mol Biol. 2005 Oct 7;352(5):1081-90. PMID:16140324 doi:10.1016/j.jmb.2005.08.002
↑ Hansson MD, Karlberg T, Soderberg CA, Rajan S, Warren MJ, Al-Karadaghi S, Rigby SE, Hansson M. Bacterial ferrochelatase turns human: Tyr13 determines the apparent metal specificity of Bacillus subtilis ferrochelatase. J Biol Inorg Chem. 2010 Nov 4. PMID:21052751 doi:10.1007/s00775-010-0720-4
↑ Dailey HA, Gerdes S, Dailey TA, Burch JS, Phillips JD. Noncanonical coproporphyrin-dependent bacterial heme biosynthesis pathway that does not use protoporphyrin. Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):2210-5. PMID:25646457 doi:10.1073/pnas.1416285112
↑ Mielcarek A, Blauenburg B, Miethke M, Marahiel MA. Molecular insights into frataxin-mediated iron supply for heme biosynthesis in Bacillus subtilis. PLoS One. 2015 Mar 31;10(3):e0122538. PMID:25826316 doi:10.1371/journal.pone.0122538
↑ Lobo SA, Scott A, Videira MA, Winpenny D, Gardner M, Palmer MJ, Schroeder S, Lawrence AD, Parkinson T, Warren MJ, Saraiva LM. Staphylococcus aureus haem biosynthesis: characterisation of the enzymes involved in final steps of the pathway. Mol Microbiol. 2015 Aug;97(3):472-87. PMID:25908396 doi:10.1111/mmi.13041
↑ Hansson M, Hederstedt L. Purification and characterisation of a water-soluble ferrochelatase from Bacillus subtilis. Eur J Biochem. 1994 Feb 15;220(1):201-8. PMID:8119288 doi:10.1111/j.1432-1033.1994.tb18615.x
↑ Lecerof D, Fodje MN, Alvarez Leon R, Olsson U, Hansson A, Sigfridsson E, Ryde U, Hansson M, Al-Karadaghi S. Metal binding to Bacillus subtilis ferrochelatase and interaction between metal sites. J Biol Inorg Chem. 2003 Apr;8(4):452-8. Epub 2003 Jan 18. PMID:12761666 doi:10.1007/s00775-002-0436-1

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ld3"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of B. subilis ferrochelatase with Zn(2+) bound at the active site.==
-<StructureSection load='1ld3' size='340' side='right' caption='[[1ld3]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='1ld3' size='340' side='right'caption='[[1ld3]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ld3]] is a 1 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LD3 FirstGlance]. <br>
+<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>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1doz|1doz]], [[1c1h|1c1h]], [[1c9e|1c9e]]</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>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferrochelatase Ferrochelatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.99.1.1 4.99.1.1] </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=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>
-<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=1ld3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ld3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ld3 RCSB], [http://www.ebi.ac.uk/pdbsum/1ld3 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/HEMH_BACSU HEMH_BACSU]] Catalyzes the ferrous insertion into protoporphyrin IX.
+[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>
+    <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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;">
@@ Line 28: / Line 28: @@
 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==
-*[[Ferrochelatase|Ferrochelatase]]
+*[[Ferrochelatase 3D structures|Ferrochelatase 3D structures]]
 == References ==
 <references/>
@@ Line 36: / Line 37: @@
 </StructureSection>
 [[Category: Bacillus subtilis]]
-[[Category: Ferrochelatase]]
+[[Category: Large Structures]]
-[[Category: Al-Karadaghi, S]]
+[[Category: Al-Karadaghi S]]
-[[Category: Fodje, M N]]
+[[Category: Fodje MN]]
-[[Category: Hansson, A]]
+[[Category: Hansson A]]
-[[Category: Hansson, M]]
+[[Category: Hansson M]]
-[[Category: Lecerof, D]]
+[[Category: Lecerof D]]
-[[Category: Leon, R A]]
+[[Category: Leon RA]]
-[[Category: Olsson, U]]
+[[Category: Olsson U]]
-[[Category: Ryde, U]]
+[[Category: Ryde U]]
-[[Category: Sigfridsson, E]]
+[[Category: Sigfridsson E]]
-[[Category: Lyase]]
-[[Category: Pi-helix]]
-[[Category: Rossmann fold]]

1ld3

From Proteopedia

Current revision

Crystal Structure of B. subilis ferrochelatase with Zn(2+) bound at the active site.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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