4zk8: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==Copper-containing nitrite reductase from thermophilic bacterium Geobacillus thermodenitrificans (Re-refined)== | ==Copper-containing nitrite reductase from thermophilic bacterium Geobacillus thermodenitrificans (Re-refined)== | ||
<StructureSection load='4zk8' size='340' side='right' caption='[[4zk8]], [[Resolution|resolution]] 1.15Å' scene=''> | <StructureSection load='4zk8' size='340' side='right' caption='[[4zk8]], [[Resolution|resolution]] 1.15Å' scene=''> | ||
| Line 4: | Line 5: | ||
<table><tr><td colspan='2'>[[4zk8]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3wko 3wko]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZK8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZK8 FirstGlance]. <br> | <table><tr><td colspan='2'>[[4zk8]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3wko 3wko]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZK8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZK8 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=4zk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zk8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4zk8 RCSB], [http://www.ebi.ac.uk/pdbsum/4zk8 PDBsum]</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=4zk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zk8 OCA], [http://pdbe.org/4zk8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zk8 RCSB], [http://www.ebi.ac.uk/pdbsum/4zk8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zk8 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 14: | Line 15: | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 4zk8" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 13:02, 10 March 2017
Copper-containing nitrite reductase from thermophilic bacterium Geobacillus thermodenitrificans (Re-refined)Copper-containing nitrite reductase from thermophilic bacterium Geobacillus thermodenitrificans (Re-refined)
Structural highlights
Publication Abstract from PubMedCopper-containing nitrite reductase (CuNIR) catalyzes the reduction of nitrite (NO(-)2) to nitric oxide (NO) during denitrification. We determined the crystal structures of CuNIR from thermophilic gram-positive bacterium, Geobacillus thermodenitrificans (GtNIR) in chloride- and formate-bound forms of wild type at 1.15 A resolution and the nitrite-bound form of the C135A mutant at 1.90 A resolution. The structure of C135A with nitrite displays a unique eta(1)-O coordination mode of nitrite at the catalytic copper site (T2Cu), which has never been observed at the T2Cu site in known wild-type CuNIRs, because the mobility of two residues essential to catalytic activity, Asp98 and His244, are sterically restricted in GtNIR by Phe109 on a characteristic loop structure that is found above Asp98 and by an unusually short CH-O hydrogen bond observed between His244 and water, respectively. A detailed comparison of the WT structure with the nitrite-bound C135A structure implies the replacement of hydrogen-bond networks around His244 and predicts the flow path of protons consumed by nitrite reduction. On the basis of these observations, the reaction mechanism of GtNIR through the eta(1)-O coordination manner is proposed. Structural insights into the function of a thermostable copper-containing nitrite reductase.,Fukuda Y, Tse KM, Lintuluoto M, Fukunishi Y, Mizohata E, Matsumura H, Takami H, Nojiri M, Inoue T J Biochem. 2014 Feb;155(2):123-35. doi: 10.1093/jb/mvt107. Epub 2013 Nov 30. PMID:24293549[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
|
| ||||||||||||||||