|
|
| Line 3: |
Line 3: |
| | <StructureSection load='6rte' size='340' side='right'caption='[[6rte]], [[Resolution|resolution]] 1.94Å' scene=''> | | <StructureSection load='6rte' size='340' side='right'caption='[[6rte]], [[Resolution|resolution]] 1.94Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6rte]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RTE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RTE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6rte]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RTE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RTE FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BU3:(R,R)-2,3-BUTANEDIOL'>BU3</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</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]] 1.94Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nirS_1, EFK27_00335, EGV95_02815, IPC669_26980, PAERUG_E15_London_28_01_14_07983, RW109_RW109_01113 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BU3:(R,R)-2,3-BUTANEDIOL'>BU3</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</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_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://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=6rte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rte OCA], [https://pdbe.org/6rte PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rte RCSB], [https://www.ebi.ac.uk/pdbsum/6rte PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rte ProSAT]</span></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=6rte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rte OCA], [http://pdbe.org/6rte PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rte RCSB], [http://www.ebi.ac.uk/pdbsum/6rte PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rte ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/NIRN_PSEAE NIRN_PSEAE] Involved in heme d1 biosynthesis (PubMed:8982003, PubMed:25204657). Catalyzes the introduction of a double bond into the propionate side chain of pyrrole ring D of dihydro-heme d1, therefore converting dihydro-heme d1 to heme d1 (PubMed:25204657).<ref>PMID:25204657</ref> <ref>PMID:8982003</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 18: |
Line 19: |
| | </div> | | </div> |
| | <div class="pdbe-citations 6rte" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6rte" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| Line 23: |
Line 27: |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Blankenfeldt, W]] | + | [[Category: Pseudomonas aeruginosa]] |
| - | [[Category: Kluenemann, T]] | + | [[Category: Blankenfeldt W]] |
| - | [[Category: Layer, G]] | + | [[Category: Kluenemann T]] |
| - | [[Category: Preuss, A]] | + | [[Category: Layer G]] |
| - | [[Category: 8-bladed beta-propeller heme d1 biosynthesis dehydrogenase]]
| + | [[Category: Preuss A]] |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
NIRN_PSEAE Involved in heme d1 biosynthesis (PubMed:8982003, PubMed:25204657). Catalyzes the introduction of a double bond into the propionate side chain of pyrrole ring D of dihydro-heme d1, therefore converting dihydro-heme d1 to heme d1 (PubMed:25204657).[1] [2]
Publication Abstract from PubMed
Many bacteria can switch from oxygen to nitrogen oxides, such as nitrate or nitrite, as terminal electron acceptors in their respiratory chain. This process is called 'denitrification' and enables biofilm formation of the opportunistic human pathogen Pseudomonas aeruginosa, making it more resilient to antibiotics and highly adaptable to different habitats. The reduction of nitrite to nitric oxide is a crucial step during denitrification. It is catalyzed by the homodimeric cytochrome cd1 nitrite reductase (NirS), which utilizes the unique isobacteriochlorin heme d1 as its reaction center. Even though the reaction mechanism of nitrite reduction is well understood, far less is known about the biosynthesis of heme d1. The last step of its biosynthesis introduces a double bond in a propionate group of the tetrapyrrole to form an acrylate group. This conversion is catalyzed by the dehydrogenase NirN via a unique reaction mechanism. To get a more detailed insight into this reaction, the crystal structures of NirN with and without bound substrate have been determined. Similar to the homodimeric NirS, the monomeric NirN consists of an eight-bladed heme d1-binding beta-propeller and a cytochrome c domain, but their relative orientation differs with respect to NirS. His147 coordinates heme d1 at the proximal side, whereas His323, which belongs to a flexible loop, binds at the distal position. Tyr461 and His417 are located next to the hydrogen atoms removed during dehydrogenation, suggesting an important role in catalysis. Activity assays with NirN variants revealed the essentiality of His147, His323 and Tyr461, but not of His417.
Crystal Structure of Dihydro-Heme d1 Dehydrogenase NirN from Pseudomonas aeruginosa Reveals Amino Acid Residues Essential for Catalysis.,Klunemann T, Preuss A, Adamczack J, Rosa LFM, Harnisch F, Layer G, Blankenfeldt W J Mol Biol. 2019 Jun 4. pii: S0022-2836(19)30336-5. doi:, 10.1016/j.jmb.2019.05.046. PMID:31173777[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Adamczack J, Hoffmann M, Papke U, Haufschildt K, Nicke T, Bröring M, Sezer M, Weimar R, Kuhlmann U, Hildebrandt P, Layer G. NirN protein from Pseudomonas aeruginosa is a novel electron-bifurcating dehydrogenase catalyzing the last step of heme d1 biosynthesis. J Biol Chem. 2014 Oct 31;289(44):30753-30762. PMID:25204657 doi:10.1074/jbc.M114.603886
- ↑ Kawasaki S, Arai H, Kodama T, Igarashi Y. Gene cluster for dissimilatory nitrite reductase (nir) from Pseudomonas aeruginosa: sequencing and identification of a locus for heme d1 biosynthesis. J Bacteriol. 1997 Jan;179(1):235-42. PMID:8982003 doi:10.1128/jb.179.1.235-242.1997
- ↑ Klunemann T, Preuss A, Adamczack J, Rosa LFM, Harnisch F, Layer G, Blankenfeldt W. Crystal Structure of Dihydro-Heme d1 Dehydrogenase NirN from Pseudomonas aeruginosa Reveals Amino Acid Residues Essential for Catalysis. J Mol Biol. 2019 Jun 4. pii: S0022-2836(19)30336-5. doi:, 10.1016/j.jmb.2019.05.046. PMID:31173777 doi:http://dx.doi.org/10.1016/j.jmb.2019.05.046
|
