|
|
| (15 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
| [[Image:2afn.gif|left|200px]]<br /><applet load="2afn" size="350" color="white" frame="true" align="right" spinBox="true"
| |
| caption="2afn, resolution 2.0Å" />
| |
| '''STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE AND A COPPER SITE MUTANT, M150E, THAT CONTAINS ZINC'''<br />
| |
|
| |
|
| ==Overview== | | ==STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE AND A COPPER SITE MUTANT, M150E, THAT CONTAINS ZINC== |
| The structures at 2.0 and 2.25 A resolution of native and recombinant, nitrite reductase from Alcaligenes faecalis show that they are identical, to each other and very similar to nitrite reductase from Achromobacter, cycloclastes. The crystallographic structure of a mutant, M150E, which, unlike the wild-type protein cannot be reduced by pseudoazurin, shows that, the glutamate replacement for methionine binds to a metal at the type I Cu, site via only one oxygen. Anomalous scattering data collected at, wavelengths of 1.040 and 1.377 A reveal that the metal at the type I site, is a Zn. No significant differences from the native structure other than, local perturbations at the type I site are seen. A local pseudo 2-fold, axis relates the two domains of different monomers which form the active, site. The two residues, Asp98 and His255, believed to be involved in, catalysis are related by this 2-fold. An unusual (+)-(+) charge, interaction between Lys269, Glu279, and His100 helps to orient the active, site Cu ligand, His100. A number of negatively charged surface residues, create an electrostatic field whose shape suggests that it may serve to, direct incoming negatively charged nitrite as well as to dock the electron, donor partner, pseudoazurin.
| | <StructureSection load='2afn' size='340' side='right'caption='[[2afn]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == |
| | <table><tr><td colspan='2'>[[2afn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1afn 1afn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AFN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AFN 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]] 2Å</td></tr> |
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=2afn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2afn OCA], [https://pdbe.org/2afn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2afn RCSB], [https://www.ebi.ac.uk/pdbsum/2afn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2afn ProSAT]</span></td></tr> |
| | </table> |
| | == Function == |
| | [https://www.uniprot.org/uniprot/NIR_ALCFA NIR_ALCFA] |
| | == 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/af/2afn_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/main_output.php?pdb_ID=2afn ConSurf]. |
| | <div style="clear:both"></div> |
|
| |
|
| ==About this Structure== | | ==See Also== |
| 2AFN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis] with <scene name='pdbligand=CU:'>CU</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure superseeds the now removed PDB entry 1AFN. Active as [http://en.wikipedia.org/wiki/Transferred_entry:_1.7.2.1 Transferred entry: 1.7.2.1], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.99.3 1.7.99.3] Known structural/functional Sites: <scene name='pdbsite=CU1:Type+I+Site+In+Monomer+A'>CU1</scene>, <scene name='pdbsite=CU2:Type+II+Site+Between+Monomers+A+And+B'>CU2</scene>, <scene name='pdbsite=CU3:Type+I+Site+In+Monomer+B'>CU3</scene>, <scene name='pdbsite=CU4:Type+II+Site+Between+Monomers+B+And+C'>CU4</scene>, <scene name='pdbsite=CU5:Type+I+Site+In+Monomer+C'>CU5</scene> and <scene name='pdbsite=CU6:Type+II+Site+Between+Monomers+C+And+A'>CU6</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AFN OCA].
| | *[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]] |
| | | __TOC__ |
| ==Reference==
| | </StructureSection> |
| Structure of Alcaligenes faecalis nitrite reductase and a copper site mutant, M150E, that contains zinc., Murphy ME, Turley S, Kukimoto M, Nishiyama M, Horinouchi S, Sasaki H, Tanokura M, Adman ET, Biochemistry. 1995 Sep 26;34(38):12107-17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7547950 7547950]
| |
| [[Category: Alcaligenes faecalis]] | | [[Category: Alcaligenes faecalis]] |
| [[Category: Single protein]] | | [[Category: Large Structures]] |
| [[Category: Transferred entry: 1.7.2.1]]
| | [[Category: Adman ET]] |
| [[Category: Adman, E.T.]] | | [[Category: Murphy MEP]] |
| [[Category: Murphy, M.E.P.]] | | [[Category: Turley S]] |
| [[Category: Turley, S.]] | |
| [[Category: CU]]
| |
| [[Category: (nitric oxide (a))]]
| |
| [[Category: copper]]
| |
| [[Category: fad]]
| |
| [[Category: flavoprotein]]
| |
| [[Category: nitrite assimilation]]
| |
| [[Category: oxidoreductase]]
| |
| | |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 10:22:54 2008''
| |