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| | ==Coproporphyrinogen III oxidase (HemN) from Escherichia coli is a Radical SAM enzyme.== | | ==Coproporphyrinogen III oxidase (HemN) from Escherichia coli is a Radical SAM enzyme.== |
| - | <StructureSection load='1olt' size='340' side='right' caption='[[1olt]], [[Resolution|resolution]] 2.07Å' scene=''> | + | <StructureSection load='1olt' size='340' side='right'caption='[[1olt]], [[Resolution|resolution]] 2.07Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1olt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OLT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OLT FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1olt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OLT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OLT FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 2.07Å</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=1olt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1olt OCA], [http://pdbe.org/1olt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1olt RCSB], [http://www.ebi.ac.uk/pdbsum/1olt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1olt ProSAT]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=1olt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1olt OCA], [https://pdbe.org/1olt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1olt RCSB], [https://www.ebi.ac.uk/pdbsum/1olt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1olt ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/HEMN_ECOLI HEMN_ECOLI]] Involved in the heme biosynthesis. Catalyzes the anaerobic oxidative decarboxylation of propionate groups of rings A and B of coproporphyrinogen-III to yield the vinyl groups in protoporphyrinogen-IX. It can use NAD or NADP, but NAD is preferred.<ref>PMID:7768836</ref> <ref>PMID:12114526</ref> | + | [https://www.uniprot.org/uniprot/HEMN_ECOLI HEMN_ECOLI] Involved in the heme biosynthesis. Catalyzes the anaerobic oxidative decarboxylation of propionate groups of rings A and B of coproporphyrinogen-III to yield the vinyl groups in protoporphyrinogen-IX. It can use NAD or NADP, but NAD is preferred.<ref>PMID:7768836</ref> <ref>PMID:12114526</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Escherichia coli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Heinz, D W]] | + | [[Category: Large Structures]] |
| - | [[Category: Jahn, D]] | + | [[Category: Heinz DW]] |
| - | [[Category: Layer, G]] | + | [[Category: Jahn D]] |
| - | [[Category: Moser, J]] | + | [[Category: Layer G]] |
| - | [[Category: Schubert, W D]] | + | [[Category: Moser J]] |
| - | [[Category: 4fe- 4s cluster]]
| + | [[Category: Schubert W-D]] |
| - | [[Category: Decarboxylase]]
| + | |
| - | [[Category: Heme biosynthesis]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Radical sam enzyme]]
| + | |
| - | [[Category: S-adenosyl-l-methionine]]
| + | |
| Structural highlights
Function
HEMN_ECOLI Involved in the heme biosynthesis. Catalyzes the anaerobic oxidative decarboxylation of propionate groups of rings A and B of coproporphyrinogen-III to yield the vinyl groups in protoporphyrinogen-IX. It can use NAD or NADP, but NAD is preferred.[1] [2]
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
'Radical SAM' enzymes generate catalytic radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. We present the first crystal structure of a Radical SAM enzyme, that of HemN, the Escherichia coli oxygen-independent coproporphyrinogen III oxidase, at 2.07 A resolution. HemN catalyzes the essential conversion of coproporphyrinogen III to protoporphyrinogen IX during heme biosynthesis. HemN binds a 4Fe-4S cluster through three cysteine residues conserved in all Radical SAM enzymes. A juxtaposed SAM coordinates the fourth Fe ion through its amide nitrogen and carboxylate oxygen. The SAM sulfonium sulfur is near both the Fe (3.5 A) and a neighboring sulfur of the cluster (3.6 A), allowing single electron transfer from the 4Fe-4S cluster to the SAM sulfonium. SAM is cleaved yielding a highly oxidizing 5'-deoxyadenosyl radical. HemN, strikingly, binds a second SAM immediately adjacent to the first. It may thus successively catalyze two propionate decarboxylations. The structure of HemN reveals the cofactor geometry required for Radical SAM catalysis and sets the stage for the development of inhibitors with antibacterial function due to the uniquely bacterial occurrence of the enzyme.
Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes.,Layer G, Moser J, Heinz DW, Jahn D, Schubert WD EMBO J. 2003 Dec 1;22(23):6214-24. PMID:14633981[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Troup B, Hungerer C, Jahn D. Cloning and characterization of the Escherichia coli hemN gene encoding the oxygen-independent coproporphyrinogen III oxidase. J Bacteriol. 1995 Jun;177(11):3326-31. PMID:7768836
- ↑ Layer G, Verfurth K, Mahlitz E, Jahn D. Oxygen-independent coproporphyrinogen-III oxidase HemN from Escherichia coli. J Biol Chem. 2002 Sep 13;277(37):34136-42. Epub 2002 Jul 11. PMID:12114526 doi:http://dx.doi.org/10.1074/jbc.M205247200
- ↑ Layer G, Moser J, Heinz DW, Jahn D, Schubert WD. Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes. EMBO J. 2003 Dec 1;22(23):6214-24. PMID:14633981 doi:10.1093/emboj/cdg598
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