View source for 5ngx


==The 1.06 A resolution structure of the L16G mutant of ferric cytochrome c prime from Alcaligenes xylosoxidans, complexed with nitrite==
<StructureSection load='5ngx' size='340' side='right'caption='[[5ngx]], [[Resolution|resolution]] 1.06&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5ngx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NGX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NGX FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.06&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></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=5ngx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ngx OCA], [https://pdbe.org/5ngx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ngx RCSB], [https://www.ebi.ac.uk/pdbsum/5ngx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ngx ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CYCP_ALCXX CYCP_ALCXX] Cytochrome c' is the most widely occurring bacterial c-type cytochrome. Cytochromes c' are high-spin proteins and the heme has no sixth ligand. Their exact function is not known.
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== Publication Abstract from PubMed ==
Nitrite coordination to heme cofactors is a key step in the anaerobic production of the signaling molecule nitric oxide (NO). An ambidentate ligand, nitrite has the potential to coordinate via the N- (nitro) or O- (nitrito) atoms in a manner that can direct its reactivity. Distinguishing nitro vs nitrito coordination, along with the influence of the surrounding protein, is therefore of particular interest. In this study, we probed Fe(III) heme-nitrite coordination in Alcaligenes xylosoxidans cytochrome c' (AXCP), an NO carrier that excludes anions in its native state but that readily binds nitrite (Kd approximately 0.5 mM) following a distal Leu16 --&gt; Gly mutation to remove distal steric constraints. Room-temperature resonance Raman spectra (407 nm excitation) identify nu(Fe-NO2), delta(ONO), and nus(NO2) nitrite ligand vibrations in solution. Illumination with 351 nm UV light results in photoconversion to {FeNO}(6) and {FeNO}(7) states, enabling FTIR measurements to distinguish nus(NO2) and nuas(NO2) vibrations from differential spectra. Density functional theory calculations highlight the connections between heme environment, nitrite coordination mode, and vibrational properties and confirm that nitrite binds to L16G AXCP exclusively through the N atom. Efforts to obtain the nitrite complex crystal structure were hampered by photochemistry in the X-ray beam. Although low dose crystal structures could be modeled with a mixed nitrite (nitro)/H2O distal population, their photosensitivity and partial occupancy underscores the value of the vibrational approach. Overall, this study sheds light on steric determinants of heme-nitrite binding and provides vibrational benchmarks for future studies of heme protein nitrite reactions.

Distinguishing Nitro vs Nitrito Coordination in Cytochrome c' Using Vibrational Spectroscopy and Density Functional Theory.,Nilsson ZN, Mandella BL, Sen K, Kekilli D, Hough MA, Moenne-Loccoz P, Strange RW, Andrew CR Inorg Chem. 2017 Nov 6;56(21):13205-13213. doi: 10.1021/acs.inorgchem.7b01945. PMID:29053273<ref>PMID:29053273</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 5ngx" style="background-color:#fffaf0;"></div>

==See Also==
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Achromobacter xylosoxidans]]
[[Category: Large Structures]]
[[Category: Horrell S]]
[[Category: Hough M]]
[[Category: Kekelli D]]
[[Category: Moreno Chicano T]]
[[Category: Strange R]]