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.

3d1i

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:50, 2 February 2022

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 Dsm 14787. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , ,
Related:	2ot4, 2zo5
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[Q5F2I3_9GAMM] Plays a role in nitrite reduction (By similarity).[SAAS:SAAS003321_004_001592]

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^[1]

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

References

↑ 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 3: / Line 3: @@
 <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/Dsm_14787 Dsm 14787]. 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/Dsm_14787 Dsm 14787]. 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='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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ot4|2ot4]], [[2zo5|2zo5]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ot4|2ot4]], [[2zo5|2zo5]]</div></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://pdbe.org/3d1i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d1i RCSB], [http://www.ebi.ac.uk/pdbsum/3d1i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3d1i 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=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/Q5F2I3_9GAMM Q5F2I3_9GAMM]] Plays a role in nitrite reduction (By similarity).[SAAS:SAAS003321_004_001592]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[Nitrite reductase|Nitrite reductase]]
+*[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]]
 == References ==
 <references/>

3d1i

From Proteopedia

Revision as of 07:50, 2 February 2022

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?)

Views

Personal tools

Navigation

Search

Toolbox