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2q3j

From Proteopedia

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Current revision

Crystal structure of the His183Ala variant of Bacillus subtilis ferrochelatase in complex with N-Methyl Mesoporphyrin

Structural highlights

2q3j 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 2.39Å
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

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.

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^[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
↑ Karlberg T, Hansson MD, Yengo RK, Johansson R, Thorvaldsen HO, Ferreira GC, Hansson M, Al-Karadaghi S. Porphyrin binding and distortion and substrate specificity in the ferrochelatase reaction: the role of active site residues. J Mol Biol. 2008 May 16;378(5):1074-83. Epub 2008 Mar 28. PMID:18423489 doi:10.1016/j.jmb.2008.03.040

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/2q3j"

Categories: Bacillus subtilis | Large Structures | Al-Karadaghi S | Karlberg T | Thorvaldsen OH

@@ Line 3: / Line 3: @@
 <StructureSection load='2q3j' size='340' side='right'caption='[[2q3j]], [[Resolution|resolution]] 2.39&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2q3j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q3J FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2q3j]] 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=2Q3J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q3J FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H02:N-METHYL+PROTOPORPHYRIN+IX+2,4-DISULFONIC+ACID'>H02</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.39&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2q2n|2q2n]], [[2q2o|2q2o]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H02:N-METHYL+PROTOPORPHYRIN+IX+2,4-DISULFONIC+ACID'>H02</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hemH, hemF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ferrochelatase Ferrochelatase], with EC number [https://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=2q3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3j OCA], [https://pdbe.org/2q3j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q3j RCSB], [https://www.ebi.ac.uk/pdbsum/2q3j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q3j ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://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]]
@@ Line 38: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Vibrio subtilis ehrenberg 1835]]
+[[Category: Bacillus subtilis]]
-[[Category: Ferrochelatase]]
 [[Category: Large Structures]]
-[[Category: Al-Karadaghi, S]]
+[[Category: Al-Karadaghi S]]
-[[Category: Karlberg, T]]
+[[Category: Karlberg T]]
-[[Category: Thorvaldsen, O H]]
+[[Category: Thorvaldsen OH]]
-[[Category: Lyase]]
-[[Category: N-memp]]
-[[Category: N-methyl mesoporphyrin ix]]
-[[Category: Pi-helix]]
-[[Category: Rossmann fold]]

2q3j

From Proteopedia

Current revision

Crystal structure of the His183Ala variant of Bacillus subtilis ferrochelatase in complex with N-Methyl Mesoporphyrin

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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