3ubr

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 3: Line 3:
<StructureSection load='3ubr' size='340' side='right'caption='[[3ubr]], [[Resolution|resolution]] 2.59&Aring;' scene=''>
<StructureSection load='3ubr' size='340' side='right'caption='[[3ubr]], [[Resolution|resolution]] 2.59&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3ubr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_700550 Atcc 700550]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UBR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UBR FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3ubr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UBR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UBR FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.59&#8491;</td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nrfA, Shewanella oneidensis, SO_3980 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70863 ATCC 700550])</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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'>[https://en.wikipedia.org/wiki/Nitrite_reductase_(cytochrome;_ammonia-forming) Nitrite reductase (cytochrome; ammonia-forming)], with EC number [https://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=3ubr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ubr OCA], [https://pdbe.org/3ubr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ubr RCSB], [https://www.ebi.ac.uk/pdbsum/3ubr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ubr ProSAT]</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=3ubr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ubr OCA], [https://pdbe.org/3ubr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ubr RCSB], [https://www.ebi.ac.uk/pdbsum/3ubr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ubr ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[https://www.uniprot.org/uniprot/NRFA_SHEON NRFA_SHEON]] Plays a role in nitrite reduction.[HAMAP-Rule:MF_01182]
+
[https://www.uniprot.org/uniprot/NRFA_SHEON NRFA_SHEON] Plays a role in nitrite reduction.[HAMAP-Rule:MF_01182]
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
The high-yield expression and purification of Shewanella oneidensis cytochrome c nitrite reductase (ccNiR) and its characterization by a variety of methods, notably Laue crystallography, are reported. A key component of the expression system is an artificial ccNiR gene in which the N-terminal signal peptide from the highly expressed S. oneidensis protein "small tetraheme c" replaces the wild-type signal peptide. This gene, inserted into the plasmid pHSG298 and expressed in S. oneidensis TSP-1 strain, generated approximately 20 mg crude ccNiR per liter of culture, compared with 0.5-1 mg/L for untransformed cells. Purified ccNiR has nitrite and hydroxylamine reductase activities comparable to those previously reported for Escherichia coli ccNiR, and is stable for over 2 weeks in pH 7 solution at 4 degrees C. UV/vis spectropotentiometric titrations and protein film voltammetry identified five independent one-electron reduction processes. Global analysis of the spectropotentiometric data also allowed determination of the extinction coefficient spectra for the five reduced ccNiR species. The characteristics of the individual extinction coefficient spectra suggest that, within each reduced species, the electrons are distributed among the various hemes, rather than being localized on specific heme centers. The purified ccNiR yielded good-quality crystals, with which the 2.59-A-resolution structure was solved at room temperature using the Laue diffraction method. The structure is similar to that of E. coli ccNiR, except in the region where the enzyme interacts with its physiological electron donor (CymA in the case of S. oneidensis ccNiR, NrfB in the case of the E. coli protein).
+
-
 
+
-
Laue crystal structure of Shewanella oneidensis cytochrome c nitrite reductase from a high-yield expression system.,Youngblut M, Judd ET, Srajer V, Sayyed B, Goelzer T, Elliott SJ, Schmidt M, Pacheco AA J Biol Inorg Chem. 2012 Mar 2. PMID:22382353<ref>PMID:22382353</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3ubr" style="background-color:#fffaf0;"></div>
+
==See Also==
==See Also==
Line 25: Line 15:
*[[Hemeproteins|Hemeproteins]]
*[[Hemeproteins|Hemeproteins]]
*[[Nitrite reductase|Nitrite reductase]]
*[[Nitrite reductase|Nitrite reductase]]
-
== References ==
 
-
<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Atcc 700550]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Elliott, S]]
+
[[Category: Shewanella oneidensis]]
-
[[Category: Goeltzner, T]]
+
[[Category: Elliott S]]
-
[[Category: Judd, E T]]
+
[[Category: Goeltzner T]]
-
[[Category: Pacheco, A]]
+
[[Category: Judd ET]]
-
[[Category: Sayed, B]]
+
[[Category: Pacheco A]]
-
[[Category: Schmidt, M]]
+
[[Category: Sayed B]]
-
[[Category: Srajer, V]]
+
[[Category: Schmidt M]]
-
[[Category: Youngblut, M]]
+
[[Category: Srajer V]]
-
[[Category: Cyma]]
+
[[Category: Youngblut M]]
-
[[Category: Deca-heme]]
+
-
[[Category: Electron transfer]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Redox]]
+

Revision as of 13:53, 14 March 2024

Laue structure of Shewanella oneidensis cytochrome-c Nitrite Reductase

PDB ID 3ubr

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/3ubr"
Personal tools