1l9r

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[[Image:1l9r.jpg|left|200px]]<br /><applet load="1l9r" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1l9r, resolution 1.78&Aring;" />
 
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'''CRYSTAL STRUCTURE OF THE I257M VARIANT OF THE COPPER-CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIS S-6'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF THE I257M VARIANT OF THE COPPER-CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIS S-6==
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Unlike the heme cd(1)-based nitrite reductase enzymes, the molecular mechanism of copper-containing nitrite reductases remains controversial. A key source of controversy is the productive binding mode of nitrite in the active site. To identify and characterize the molecular determinants associated with nitrite binding, we applied a combinatorial mutagenesis approach to generate a small library of six variants at position 257 in nitrite reductase from Alcaligenes faecalis S-6. The activities of these six variants span nearly two orders of magnitude with one variant, I257V, the only observed natural substitution for Ile257, showing greater activity than the native enzyme. High-resolution (&gt; 1.8 A) nitrite-soaked crystal structures of these variants display different modes of nitrite binding that correlate well with the altered activities. These studies identify for the first time that the highly conserved Ile257 in the native enzyme is a key molecular determinant in directing a catalytically competent mode of nitrite binding in the active site. The O-coordinate bidentate binding mode of nitrite observed in native and mutant forms with high activity supports a catalytic model distinct from the heme cd(1) NiRs. (The atomic coordinates for I257V[NO(2)(-)], I257L[NO(2)(-)], I257A[NO(2)(-)], I257T[NO(2)(-)], I257M[NO(2)(-)] and I257G[NO(2)(-)] AfNiR have been deposited in the Protein Data Bank [PDB identification codes are listed in Table 2].)
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<StructureSection load='1l9r' size='340' side='right'caption='[[1l9r]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1l9r]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L9R FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.78&#8491;</td></tr>
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<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>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1l9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l9r OCA], [https://pdbe.org/1l9r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l9r RCSB], [https://www.ebi.ac.uk/pdbsum/1l9r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l9r ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NIR_ALCFA NIR_ALCFA]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l9/1l9r_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1l9r ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1L9R 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> and <scene name='pdbligand=NO2:'>NO2</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9R OCA].
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*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Directing the mode of nitrite binding to a copper-containing nitrite reductase from Alcaligenes faecalis S-6: characterization of an active site isoleucine., Boulanger MJ, Murphy ME, Protein Sci. 2003 Feb;12(2):248-56. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12538888 12538888]
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[[Category: Alcaligenes faecalis]]
[[Category: Alcaligenes faecalis]]
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[[Category: Nitrite reductase (NO-forming)]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Boulanger MJ]]
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[[Category: Boulanger, M J.]]
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[[Category: Murphy MEP]]
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[[Category: Murphy, M E.P.]]
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[[Category: CU]]
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[[Category: NO2]]
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[[Category: cupredoxin fold]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:42:52 2008''
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Current revision

CRYSTAL STRUCTURE OF THE I257M VARIANT OF THE COPPER-CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIS S-6

PDB ID 1l9r

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