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1ogy

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Revision as of 07:31, 7 February 2018

Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides

Structural highlights

1ogy is a 16 chain structure with sequence from "rhodococcus_capsulatus"_molisch_1907 "rhodococcus capsulatus" molisch 1907. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Activity:	Nitrate reductase, with EC number 1.7.99.4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[NAPA_RHOS4] Catalytic subunit of the periplasmic nitrate reductase (NAP). Only expressed at high levels during aerobic growth. NapAB complex receives electrons from the membrane-anchored tetraheme protein NapC, thus allowing electron flow between membrane and periplasm. Essential function for nitrate assimilation and may have a role in anaerobic metabolism. [NAPB_RHOSH] Electron transfer subunit of the periplasmic nitrate reductase complex NapAB. Receives electrons from the membrane-anchored tetraheme c-type NapC protein and transfers these to NapA subunit, thus allowing electron flow between membrane and periplasm. Essential for periplasmic nitrate reduction with nitrate as the terminal electron acceptor.^[1] ^[2] ^[3] ^[4]

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

The structure of the respiratory nitrate reductase (NapAB) from Rhodobacter sphaeroides, the periplasmic heterodimeric enzyme responsible for the first step in the denitrification process, has been determined at a resolution of 3.2 A. The di-heme electron transfer small subunit NapB binds to the large subunit with heme II in close proximity to the [4Fe-4S] cluster of NapA. A total of 57 residues at the N- and C-terminal extremities of NapB adopt an extended conformation, embracing the NapA subunit and largely contributing to the total area of 5,900 A(2) buried in the complex. Complex formation was studied further by measuring the variation of the redox potentials of all the cofactors upon binding. The marked effects observed are interpreted in light of the three-dimensional structure and depict a plasticity that contributes to an efficient electron transfer in the complex from the heme I of NapB to the molybdenum catalytic site of NapA.

Structural and redox plasticity in the heterodimeric periplasmic nitrate reductase.,Arnoux P, Sabaty M, Alric J, Frangioni B, Guigliarelli B, Adriano JM, Pignol D Nat Struct Biol. 2003 Nov;10(11):928-34. Epub 2003 Oct 5. PMID:14528294^[5]

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

References

↑ Liu HP, Takio S, Satoh T, Yamamoto I. Involvement in denitrification of the napKEFDABC genes encoding the periplasmic nitrate reductase system in the denitrifying phototrophic bacterium Rhodobacter sphaeroides f. sp. denitrificans. Biosci Biotechnol Biochem. 1999 Mar;63(3):530-6. PMID:10227138
↑ Sabaty M, Schwintner C, Cahors S, Richaud P, Vermeglio A. Nitrite and nitrous oxide reductase regulation by nitrogen oxides in Rhodobacter sphaeroides f. sp. denitrificans IL106. J Bacteriol. 1999 Oct;181(19):6028-32. PMID:10498715
↑ Pignol D, Adriano JM, Fontecilla-Camps JC, Sabaty M. Crystallization and preliminary X-ray analysis of the periplasmic nitrate reductase (NapA-NapB complex) from Rhodobacter sphaeroides f. sp. denitrificans. Acta Crystallogr D Biol Crystallogr. 2001 Dec;57(Pt 12):1900-2. Epub 2001, Nov 21. PMID:11717511
↑ Tabata A, Yamamoto I, Matsuzaki M, Satoh T. Differential regulation of periplasmic nitrate reductase gene (napKEFDABC) expression between aerobiosis and anaerobiosis with nitrate in a denitrifying phototroph Rhodobacter sphaeroides f. sp. denitrificans. Arch Microbiol. 2005 Nov;184(2):108-16. Epub 2005 Oct 21. PMID:16136296 doi:http://dx.doi.org/10.1007/s00203-005-0029-9
↑ Arnoux P, Sabaty M, Alric J, Frangioni B, Guigliarelli B, Adriano JM, Pignol D. Structural and redox plasticity in the heterodimeric periplasmic nitrate reductase. Nat Struct Biol. 2003 Nov;10(11):928-34. Epub 2003 Oct 5. PMID:14528294 doi:10.1038/nsb994

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ogy"

@@ Line 1: / Line 1: @@
-==CRYSTAL STRUCTURE OF THE HETERODIMERIC NITRATE REDUCTASE FROM RHODOBACTER SPHAEROIDES==
+==Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides==
 <StructureSection load='1ogy' size='340' side='right' caption='[[1ogy]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=MO:MOLYBDENUM+ATOM'>MO</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrate_reductase Nitrate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.99.4 1.7.99.4] </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=1ogy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ogy OCA], [http://pdbe.org/1ogy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ogy RCSB], [http://www.ebi.ac.uk/pdbsum/1ogy PDBsum]</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=1ogy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ogy OCA], [http://pdbe.org/1ogy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ogy RCSB], [http://www.ebi.ac.uk/pdbsum/1ogy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ogy ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/og/1ogy_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/og/1ogy_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 28: / Line 29: @@
 </div>
 <div class="pdbe-citations 1ogy" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Cytochrome c|Cytochrome c]]
-*[[Nitrate reductase|Nitrate reductase]]
 == References ==
 <references/>

1ogy

From Proteopedia

Revision as of 07:31, 7 February 2018

Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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