2h1v: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|200px<br /><applet load="2h1v" size="450" color="white" frame="true" align="right" spinBox="true" caption="2h1v, resolution 1.20Å" /> '''Crystal structure of...
 
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2h1v.gif|left|200px]]<br /><applet load="2h1v" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2h1v, resolution 1.20&Aring;" />
'''Crystal structure of the Lys87Ala mutant variant of Bacillus subtilis ferrochelatase'''<br />


==Overview==
==Crystal structure of the Lys87Ala mutant variant of Bacillus subtilis ferrochelatase==
Ferrochelatase catalyzes the terminal step in the heme biosynthetic, pathway, i.e., the incorporation of Fe(II) into protoporphyrin IX. Various, biochemical and biophysical methods have been used to probe the enzyme for, metal binding residues and the location of the active site. However, the, location of the metal binding site and the path of the metal into the, porphyrin are still disputed. Using site-directed mutagenesis on Bacillus, subtilis ferrochelatase we demonstrate that exchange of the conserved, residues His183 and Glu264 affects the metal affinity of the enzyme. We, also present the first X-ray crystal structure of ferrochelatase with, iron. Only a single iron was found in the active site, coordinated in a, square pyramidal fashion by two amino acid residues, His183 and Glu264, and three water molecules. This iron was not present in the structure of a, His183Ala modified ferrochelatase. The results strongly suggest that the, insertion of a metal ion into protoporphyrin IX by ferrochelatase occurs, from a metal binding site represented by His183 and Glu264.
<StructureSection load='2h1v' size='340' side='right'caption='[[2h1v]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2h1v]] 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=2H1V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H1V FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=2h1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h1v OCA], [https://pdbe.org/2h1v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h1v RCSB], [https://www.ebi.ac.uk/pdbsum/2h1v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h1v 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/h1/2h1v_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=2h1v ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ferrochelatase catalyzes the terminal step in the heme biosynthetic pathway, i.e., the incorporation of Fe(II) into protoporphyrin IX. Various biochemical and biophysical methods have been used to probe the enzyme for metal binding residues and the location of the active site. However, the location of the metal binding site and the path of the metal into the porphyrin are still disputed. Using site-directed mutagenesis on Bacillus subtilis ferrochelatase we demonstrate that exchange of the conserved residues His183 and Glu264 affects the metal affinity of the enzyme. We also present the first X-ray crystal structure of ferrochelatase with iron. Only a single iron was found in the active site, coordinated in a square pyramidal fashion by two amino acid residues, His183 and Glu264, and three water molecules. This iron was not present in the structure of a His183Ala modified ferrochelatase. The results strongly suggest that the insertion of a metal ion into protoporphyrin IX by ferrochelatase occurs from a metal binding site represented by His183 and Glu264.


==About this Structure==
Amino acid residues His183 and Glu264 in Bacillus subtilis ferrochelatase direct and facilitate the insertion of metal ion into protoporphyrin IX.,Hansson MD, Karlberg T, Rahardja MA, Al-Karadaghi S, Hansson M Biochemistry. 2007 Jan 9;46(1):87-94. PMID:17198378<ref>PMID:17198378</ref>
2H1V is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with MG as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2H1V OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Amino acid residues His183 and Glu264 in Bacillus subtilis ferrochelatase direct and facilitate the insertion of metal ion into protoporphyrin IX., Hansson MD, Karlberg T, Rahardja MA, Al-Karadaghi S, Hansson M, Biochemistry. 2007 Jan 9;46(1):87-94. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17198378 17198378]
</div>
<div class="pdbe-citations 2h1v" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Ferrochelatase 3D structures|Ferrochelatase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
[[Category: Ferrochelatase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Al-Karadaghi S]]
[[Category: Al-Karadaghi, S.]]
[[Category: Arys Rahardja M]]
[[Category: Hansson, M.]]
[[Category: Hansson M]]
[[Category: Hansson, M.D.]]
[[Category: Hansson MD]]
[[Category: Karlberg, T.]]
[[Category: Karlberg T]]
[[Category: Rahardja, M.Arys.]]
[[Category: MG]]
[[Category: pi-helix]]
[[Category: rossman fold]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 11:30:16 2007''

Latest revision as of 12:50, 30 August 2023

Crystal structure of the Lys87Ala mutant variant of Bacillus subtilis ferrochelataseCrystal structure of the Lys87Ala mutant variant of Bacillus subtilis ferrochelatase

Structural highlights

2h1v 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 1.2Å
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 catalyzes the terminal step in the heme biosynthetic pathway, i.e., the incorporation of Fe(II) into protoporphyrin IX. Various biochemical and biophysical methods have been used to probe the enzyme for metal binding residues and the location of the active site. However, the location of the metal binding site and the path of the metal into the porphyrin are still disputed. Using site-directed mutagenesis on Bacillus subtilis ferrochelatase we demonstrate that exchange of the conserved residues His183 and Glu264 affects the metal affinity of the enzyme. We also present the first X-ray crystal structure of ferrochelatase with iron. Only a single iron was found in the active site, coordinated in a square pyramidal fashion by two amino acid residues, His183 and Glu264, and three water molecules. This iron was not present in the structure of a His183Ala modified ferrochelatase. The results strongly suggest that the insertion of a metal ion into protoporphyrin IX by ferrochelatase occurs from a metal binding site represented by His183 and Glu264.

Amino acid residues His183 and Glu264 in Bacillus subtilis ferrochelatase direct and facilitate the insertion of metal ion into protoporphyrin IX.,Hansson MD, Karlberg T, Rahardja MA, Al-Karadaghi S, Hansson M Biochemistry. 2007 Jan 9;46(1):87-94. PMID:17198378[9]

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

See Also

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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
  4. ↑ 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
  5. ↑ 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
  6. ↑ 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
  7. ↑ 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
  8. ↑ 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
  9. ↑ Hansson MD, Karlberg T, Rahardja MA, Al-Karadaghi S, Hansson M. Amino acid residues His183 and Glu264 in Bacillus subtilis ferrochelatase direct and facilitate the insertion of metal ion into protoporphyrin IX. Biochemistry. 2007 Jan 9;46(1):87-94. PMID:17198378 doi:10.1021/bi061760a

2h1v, resolution 1.20Å

Drag the structure with the mouse to rotate

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

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2h1v&oldid=3850734"