This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3ayf

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:02, 13 March 2024) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
==Crystal structure of nitric oxide reductase==
==Crystal structure of nitric oxide reductase==
-
<StructureSection load='3ayf' size='340' side='right' caption='[[3ayf]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+
<StructureSection load='3ayf' size='340' side='right'caption='[[3ayf]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3ayf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AYF FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3ayf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AYF FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=LOP:(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL+(9Z)-OCTADEC-9-ENOATE'>LOP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.5&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ayg|3ayg]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=LOP:(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL+(9Z)-OCTADEC-9-ENOATE'>LOP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">norZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</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=3ayf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ayf OCA], [https://pdbe.org/3ayf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ayf RCSB], [https://www.ebi.ac.uk/pdbsum/3ayf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ayf 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=3ayf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ayf OCA], [http://pdbe.org/3ayf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ayf RCSB], [http://www.ebi.ac.uk/pdbsum/3ayf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ayf ProSAT]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/B3Y963_GEOSE B3Y963_GEOSE]
-
The structure of quinol-dependent nitric oxide reductase (qNOR) from G. stearothermophilus, which catalyzes the reduction of NO to produce the major ozone-depleting gas N(2)O, has been characterized at 2.5 A resolution. The overall fold of qNOR is similar to that of cytochrome c-dependent NOR (cNOR), and some structural features that are characteristic of cNOR, such as the calcium binding site and hydrophilic cytochrome c domain, are observed in qNOR, even though it harbors no heme c. In contrast to cNOR, structure-based mutagenesis and molecular dynamics simulation studies of qNOR suggest that a water channel from the cytoplasm can serve as a proton transfer pathway for the catalytic reaction. Further structural comparison of qNOR with cNOR and aerobic and microaerobic respiratory oxidases elucidates their evolutionary relationship and possible functional conversions.
+
-
 
+
-
Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus.,Matsumoto Y, Tosha T, Pisliakov AV, Hino T, Sugimoto H, Nagano S, Sugita Y, Shiro Y Nat Struct Mol Biol. 2012 Jan 22;19(2):238-45. doi: 10.1038/nsmb.2213. PMID:22266822<ref>PMID:22266822</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3ayf" style="background-color:#fffaf0;"></div>
+
==See Also==
==See Also==
-
*[[Nitric reductase|Nitric reductase]]
+
*[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]]
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Atcc 12980]]
+
[[Category: Geobacillus stearothermophilus]]
-
[[Category: Hino, T]]
+
[[Category: Large Structures]]
-
[[Category: Matsumoto, Y]]
+
[[Category: Hino T]]
-
[[Category: Nagano, S]]
+
[[Category: Matsumoto Y]]
-
[[Category: Pisliakov, A V]]
+
[[Category: Nagano S]]
-
[[Category: Shiro, Y]]
+
[[Category: Pisliakov AV]]
-
[[Category: Sugimoti, H]]
+
[[Category: Shiro Y]]
-
[[Category: Sugita, Y]]
+
[[Category: Sugimoti H]]
-
[[Category: Tosha, T]]
+
[[Category: Sugita Y]]
-
[[Category: Oxidoreductase]]
+
[[Category: Tosha T]]

Current revision

Crystal structure of nitric oxide reductase

PDB ID 3ayf

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ayf"
Personal tools