3d1i

From Proteopedia

(Difference between revisions)

Current revision

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite

Structural highlights

3d1i is a 2 chain structure with sequence from Thioalkalivibrio nitratireducens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NIR_THIND Catalyzes the reduction of nitrite to ammonia, consuming six electrons in the process (PubMed:16500161, PubMed:22281743). Has very low activity toward hydroxylamine (PubMed:16500161). Has even lower activity toward sulfite (PubMed:16500161, PubMed:22281743). Sulfite reductase activity is maximal at neutral pH (PubMed:20944237).^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Bacterial pentaheme cytochrome c nitrite reductases (NrfAs) are key enzymes involved in the terminal step of dissimilatory nitrite reduction of the nitrogen cycle. Their structure and functions are well studied. Recently, a novel octaheme cytochrome c nitrite reductase (TvNiR) has been isolated from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens. Here we present high-resolution crystal structures of the apoenzyme and its complexes with the substrate (nitrite) and the inhibitor (azide). Both in the crystalline state and in solution, TvNiR exists as a stable hexamer containing 48 hemes-the largest number of hemes accommodated within one protein molecule known to date. The subunit of TvNiR consists of two domains. The N-terminal domain has a unique fold and contains three hemes. The catalytic C-terminal domain hosts the remaining five hemes, their arrangement, including the catalytic heme, being identical to that found in NrfAs. The complete set of eight hemes forms a spatial pattern characteristic of other multiheme proteins, including structurally characterized octaheme cytochromes. The catalytic machinery of TvNiR resembles that of NrfAs. It comprises the lysine residue at the proximal position of the catalytic heme, the catalytic triad of tyrosine, histidine, and arginine at the distal side, channels for the substrate and product transport with a characteristic gradient of electrostatic potential, and, finally, two conserved Ca(2+)-binding sites. However, TvNiR has a number of special structural features, including a covalent bond between the catalytic tyrosine and the adjacent cysteine and the unusual topography of the product channels that open into the void interior space of the protein hexamer. The role of these characteristic structural features in the catalysis by this enzyme is discussed.

High-resolution structural analysis of a novel octaheme cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens.,Polyakov KM, Boyko KM, Tikhonova TV, Slutsky A, Antipov AN, Zvyagilskaya RA, Popov AN, Bourenkov GP, Lamzin VS, Popov VO J Mol Biol. 2009 Jun 26;389(5):846-62. Epub 2009 Apr 23. PMID:19393666^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Tikhonova TV, Slutsky A, Antipov AN, Boyko KM, Polyakov KM, Sorokin DY, Zvyagilskaya RA, Popov VO. Molecular and catalytic properties of a novel cytochrome c nitrite reductase from nitrate-reducing haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio nitratireducens. Biochim Biophys Acta. 2006 Apr;1764(4):715-23. Epub 2006 Feb 9. PMID:16500161 doi:http://dx.doi.org/10.1016/j.bbapap.2005.12.021
↑ Trofimov AA, Polyakov KM, Boyko KM, Tikhonova TV, Safonova TN, Tikhonov AV, Popov AN, Popov VO. Structures of complexes of octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens with sulfite and cyanide. Acta Crystallogr D Biol Crystallogr. 2010 Oct;66(Pt 10):1043-7. Epub 2010, Sep 18. PMID:20944237 doi:10.1107/S0907444910031665
↑ Trofimov AA, Polyakov KM, Tikhonova TV, Tikhonov AV, Safonova TN, Boyko KM, Dorovatovskii PV, Popov VO. Covalent modifications of the catalytic tyrosine in octahaem cytochrome c nitrite reductase and their effect on the enzyme activity. Acta Crystallogr D Biol Crystallogr. 2012 Feb;68(Pt 2):144-53. Epub 2012, Jan 13. PMID:22281743 doi:10.1107/S0907444911052632
↑ Polyakov KM, Boyko KM, Tikhonova TV, Slutsky A, Antipov AN, Zvyagilskaya RA, Popov AN, Bourenkov GP, Lamzin VS, Popov VO. High-resolution structural analysis of a novel octaheme cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens. J Mol Biol. 2009 Jun 26;389(5):846-62. Epub 2009 Apr 23. PMID:19393666 doi:10.1016/j.jmb.2009.04.037

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3d1i"

@@ Line 1: / Line 1: @@
 ==Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite==
-<StructureSection load='3d1i' size='340' side='right' caption='[[3d1i]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='3d1i' size='340' side='right'caption='[[3d1i]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3d1i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thioalkalivibrio_nitratireducens Thioalkalivibrio nitratireducens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D1I FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3d1i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thioalkalivibrio_nitratireducens Thioalkalivibrio nitratireducens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D1I FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</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]] 1.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ot4|2ot4]], [[2zo5|2zo5]]</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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</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=3d1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d1i RCSB], [http://www.ebi.ac.uk/pdbsum/3d1i PDBsum]</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=3d1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1i OCA], [https://pdbe.org/3d1i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d1i RCSB], [https://www.ebi.ac.uk/pdbsum/3d1i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d1i ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Q5F2I3_9GAMM Q5F2I3_9GAMM]] Plays a role in nitrite reduction (By similarity).[SAAS:SAAS003321_004_001592]
+[https://www.uniprot.org/uniprot/NIR_THIND NIR_THIND] Catalyzes the reduction of nitrite to ammonia, consuming six electrons in the process (PubMed:16500161, PubMed:22281743). Has very low activity toward hydroxylamine (PubMed:16500161). Has even lower activity toward sulfite (PubMed:16500161, PubMed:22281743). Sulfite reductase activity is maximal at neutral pH (PubMed:20944237).<ref>PMID:16500161</ref> <ref>PMID:20944237</ref> <ref>PMID:22281743</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d1/3d1i_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d1/3d1i_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3d1i ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3d1i" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Nitric reductase|Nitric reductase]]
+*[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Thioalkalivibrio nitratireducens]]
-[[Category: Antipov, A N]]
+[[Category: Antipov AN]]
-[[Category: Bourenkov, G P]]
+[[Category: Bourenkov GP]]
-[[Category: Boyko, K M]]
+[[Category: Boyko KM]]
-[[Category: Lamzin, V S]]
+[[Category: Lamzin VS]]
-[[Category: Polyakov, K M]]
+[[Category: Polyakov KM]]
-[[Category: Popov, A N]]
+[[Category: Popov AN]]
-[[Category: Popov, V O]]
+[[Category: Popov VO]]
-[[Category: Slutsky, A]]
+[[Category: Slutsky A]]
-[[Category: Tikhonova, T V]]
+[[Category: Tikhonova TV]]
-[[Category: Zvyagilskaya, R A]]
+[[Category: Zvyagilskaya RA]]
-[[Category: Cytochrome c nitrite reductase]]
-[[Category: Nrfa]]
-[[Category: Oxidoreductase]]
-[[Category: Sulfite reductase]]

3d1i

From Proteopedia

Current revision

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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