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| | <StructureSection load='6v0a' size='340' side='right'caption='[[6v0a]], [[Resolution|resolution]] 2.55Å' scene=''> | | <StructureSection load='6v0a' size='340' side='right'caption='[[6v0a]], [[Resolution|resolution]] 2.55Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6v0a]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geols Geols]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V0A OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V0A FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6v0a]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichlorobacter_lovleyi_SZ Trichlorobacter lovleyi SZ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V0A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6V0A FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.55Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Glov_1042 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=398767 GEOLS])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(cytochrome;_ammonia-forming) Nitrite reductase (cytochrome; ammonia-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.2 1.7.2.2] </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=6v0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v0a OCA], [https://pdbe.org/6v0a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6v0a RCSB], [https://www.ebi.ac.uk/pdbsum/6v0a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6v0a ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6v0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v0a OCA], [http://pdbe.org/6v0a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v0a RCSB], [http://www.ebi.ac.uk/pdbsum/6v0a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v0a ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/B3E641_TRIL1 B3E641_TRIL1] |
| - | Cytochrome c nitrite reductase (NrfA) catalyzes the reduction of nitrite to ammonium in the dissimilatory nitrate reduction to ammonium (DNRA) pathway, a process that competes with denitrification, conserves nitrogen, and minimizes nutrient loss in soils. The environmental bacterium Geobacter lovleyi has recently been recognized as a key driver of DNRA in nature, but its enzymatic pathway is still uncharacterized. To address this limitation, here we overexpressed, purified, and characterized G. lovleyi NrfA. We observed that the enzyme crystallizes as a dimer, but remains monomeric in solution. Importantly, its crystal structure at 2.55 A resolution revealed the presence of an arginine residue in the region otherwise occupied by calcium in canonical NrfA enzymes. The presence of EDTA did not affect the activity of G. lovleyi NrfA, and site-directed mutagenesis of this arginine reduced enzymatic activity < 3% of the wild-type levels. Phylogenetic analysis revealed four separate emergences of Arg-containing NrfA enzymes. Thus, the Ca(2+)-independent, Arg-containing NrfA from G. lovleyi represents a new subclass of cytochrome c nitrite reductase. Most genera from the exclusive clades of Arg-containing NrfA proteins are also represented in clades containing Ca(2+)-dependent enzymes, suggesting convergent evolution.
| + | |
| | | | |
| - | Cytochrome c nitrite reductase from the bacterium Geobacter lovleyi represents a new NrfA subclass.,Campecino J, Lagishetty S, Wawrzak Z, Sosa Alfaro V, Lehnert N, Reguera G, Hu J, Hegg EL J Biol Chem. 2020 Jun 9. pii: RA120.013981. doi: 10.1074/jbc.RA120.013981. PMID:32518164<ref>PMID:32518164</ref>
| + | ==See Also== |
| - | | + | *[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]] |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 6v0a" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Geols]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Campecino, J]] | + | [[Category: Trichlorobacter lovleyi SZ]] |
| - | [[Category: Hegg, L H]] | + | [[Category: Campecino J]] |
| - | [[Category: Hu, J]]
| + | [[Category: Hegg LH]] |
| - | [[Category: Satyanarayana, L]] | + | [[Category: Hu J]] |
| - | [[Category: Ammonia-forming]] | + | [[Category: Satyanarayana L]] |
| - | [[Category: Cytochrome c nitrite reductase]] | + | |
| - | [[Category: Oxidoreductase]]
| + | |
