1j9t: Difference between revisions

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New page: left|200px<br /><applet load="1j9t" size="450" color="white" frame="true" align="right" spinBox="true" caption="1j9t, resolution 1.95Å" /> '''Crystal structure of...
 
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[[Image:1j9t.gif|left|200px]]<br /><applet load="1j9t" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1j9t, resolution 1.95&Aring;" />
'''Crystal structure of nitrite soaked reduced H255N AFNIR'''<br />


==Overview==
==Crystal structure of nitrite soaked reduced H255N AFNIR==
High-resolution nitrite soaked oxidized and reduced crystal structures of, two active site mutants, D98N and H255N, of nitrite reductase (NIR) from, Alcaligenes faecalis S-6 were determined to better than 2.0 A resolution., In the oxidized D98N nitrite-soaked structures, nitrite is coordinated to, the type II copper via its oxygen atoms in an asymmetric bidentate manner;, however, elevated B-factors and weak electron density indicate that both, nitrite and Asn98 are less ordered than in the native enzyme. This, disorder likely results from the inability of the N delta 2 atom of Asn98, to form a hydrogen bond with the bound protonated nitrite, indicating that, the hydrogen bond between Asp98 and nitrite in the native NIR structure is, essential in anchoring nitrite in the active site for catalysis. In the, oxidized nitrite soaked H255N crystal structure, nitrite does not displace, the ligand water and is instead coordinated in an alternative mode via a, single oxygen to the type II copper. His255 is clearly essential in, defining the nitrite binding site despite the lack of direct interaction, with the substrate in the native enzyme. The resulting pentacoordinate, copper site in the H255N structure also serves as a model for a proposed, transient intermediate in the catalytic mechanism consisting of a hydroxyl, and nitric oxide molecule coordinated to the copper. The formation of an, unusual dinuclear type I copper site in the reduced nitrite soaked D98N, and H255N crystal structures may represent an evolutionary link between, the mononuclear type I copper centers and dinuclear Cu(A) sites.
<StructureSection load='1j9t' size='340' side='right'caption='[[1j9t]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1j9t]] 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=1J9T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J9T 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]] 1.95&#8491;</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>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</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=1j9t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j9t OCA], [https://pdbe.org/1j9t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j9t RCSB], [https://www.ebi.ac.uk/pdbsum/1j9t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j9t 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/j9/1j9t_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=1j9t ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1J9T 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 CU and NO2 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1J9T OCA].
*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Alternate substrate binding modes to two mutant (D98N and H255N) forms of nitrite reductase from Alcaligenes faecalis S-6: structural model of a transient catalytic intermediate., Boulanger MJ, Murphy ME, Biochemistry. 2001 Aug 7;40(31):9132-41. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11478880 11478880]
[[Category: Alcaligenes faecalis]]
[[Category: Alcaligenes faecalis]]
[[Category: Nitrite reductase (NO-forming)]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Boulanger MJ]]
[[Category: Boulanger, M.J.]]
[[Category: Murphy ME]]
[[Category: Murphy, M.E.]]
[[Category: CU]]
[[Category: NO2]]
[[Category: cupredoxin fold nitrite copper]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:02:17 2007''

Latest revision as of 10:38, 7 February 2024

Crystal structure of nitrite soaked reduced H255N AFNIRCrystal structure of nitrite soaked reduced H255N AFNIR

Structural highlights

1j9t is a 3 chain structure with sequence from Alcaligenes faecalis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.95Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NIR_ALCFA

Evolutionary Conservation

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

See Also

1j9t, resolution 1.95Å

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