7p2f: Difference between revisions
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==Green-type copper-nitrite reductase from Sinorhizobium meliloti 2011== | ==Green-type copper-nitrite reductase from Sinorhizobium meliloti 2011== | ||
<StructureSection load='7p2f' size='340' side='right'caption='[[7p2f]]' scene=''> | <StructureSection load='7p2f' size='340' side='right'caption='[[7p2f]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P2F FirstGlance]. <br> | <table><tr><td colspan='2'>[[7p2f]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P2F FirstGlance]. <br> | ||
</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=7p2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p2f OCA], [https://pdbe.org/7p2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p2f RCSB], [https://www.ebi.ac.uk/pdbsum/7p2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p2f ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </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=7p2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p2f OCA], [https://pdbe.org/7p2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p2f RCSB], [https://www.ebi.ac.uk/pdbsum/7p2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p2f ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
We report the crystal structure of the copper-containing nitrite reductase (NirK) from the Gram-negative bacterium Sinorhizobium meliloti 2011 (Sm), together with complex structural alignment and docking studies with both non-cognate and the physiologically related pseudoazurins, SmPaz1 and SmPaz2, respectively. S. meliloti is a rhizobacterium used for the formulation of Medicago sativa bionoculants, and SmNirK plays a key role in this symbiosis through the denitrification pathway. The structure of SmNirK, solved at a resolution of 2.5 A, showed a striking resemblance with the overall structure of the well-known Class I NirKs composed of two Greek key beta-barrel domains. The activity of SmNirK is ~12% of the activity reported for classical NirKs, which could be attributed to several factors such as subtle structural differences in the secondary proton channel, solvent accessibility of the substrate channel, and that the denitrifying activity has to be finely regulated within the endosymbiont. In vitro kinetics performed in homogenous and heterogeneous media showed that both SmPaz1 and SmPaz2, which are coded in different regions of the genome, donate electrons to SmNirK with similar performance. Even though the energetics of the interprotein electron transfer (ET) process is not favorable with either electron donors, adduct formation mediated by conserved residues allows minimizing the distance between the copper centers involved in the interprotein ET process. | |||
Copper nitrite reductase from Sinorhizobium meliloti 2011: Crystal structure and interaction with the physiological versus a nonmetabolically related cupredoxin-like mediator.,Ramirez CS, Tolmie C, Opperman DJ, Gonzalez PJ, Rivas MG, Brondino CD, Ferroni FM Protein Sci. 2021 Sep 25. doi: 10.1002/pro.4195. PMID:34562300<ref>PMID:34562300</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7p2f" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Ferroni | [[Category: Ferroni, F M]] | ||
[[Category: Opperman | [[Category: Opperman, D J]] | ||
[[Category: Tolmie C]] | [[Category: Tolmie, C]] | ||
[[Category: Denitrification pathway]] | |||
[[Category: Greek key b-barrel domain]] | |||
[[Category: Metal binding protein]] | |||
[[Category: Nitrite reductase]] | |||
Revision as of 18:54, 27 October 2021
Green-type copper-nitrite reductase from Sinorhizobium meliloti 2011Green-type copper-nitrite reductase from Sinorhizobium meliloti 2011
Structural highlights
Publication Abstract from PubMedWe report the crystal structure of the copper-containing nitrite reductase (NirK) from the Gram-negative bacterium Sinorhizobium meliloti 2011 (Sm), together with complex structural alignment and docking studies with both non-cognate and the physiologically related pseudoazurins, SmPaz1 and SmPaz2, respectively. S. meliloti is a rhizobacterium used for the formulation of Medicago sativa bionoculants, and SmNirK plays a key role in this symbiosis through the denitrification pathway. The structure of SmNirK, solved at a resolution of 2.5 A, showed a striking resemblance with the overall structure of the well-known Class I NirKs composed of two Greek key beta-barrel domains. The activity of SmNirK is ~12% of the activity reported for classical NirKs, which could be attributed to several factors such as subtle structural differences in the secondary proton channel, solvent accessibility of the substrate channel, and that the denitrifying activity has to be finely regulated within the endosymbiont. In vitro kinetics performed in homogenous and heterogeneous media showed that both SmPaz1 and SmPaz2, which are coded in different regions of the genome, donate electrons to SmNirK with similar performance. Even though the energetics of the interprotein electron transfer (ET) process is not favorable with either electron donors, adduct formation mediated by conserved residues allows minimizing the distance between the copper centers involved in the interprotein ET process. Copper nitrite reductase from Sinorhizobium meliloti 2011: Crystal structure and interaction with the physiological versus a nonmetabolically related cupredoxin-like mediator.,Ramirez CS, Tolmie C, Opperman DJ, Gonzalez PJ, Rivas MG, Brondino CD, Ferroni FM Protein Sci. 2021 Sep 25. doi: 10.1002/pro.4195. PMID:34562300[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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