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.


1nie

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:56, 14 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1nie.jpg|left|200px]]
 
-
{{Structure
+
==THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES, WITH NITRITE BOUND AND WITH TYPE II CU DEPLETED==
-
|PDB= 1nie |SIZE=350|CAPTION= <scene name='initialview01'>1nie</scene>, resolution 1.9&Aring;
+
<StructureSection load='1nie' size='340' side='right'caption='[[1nie]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>
+
<table><tr><td colspan='2'>[[1nie]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NIE FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[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] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-
|GENE=
+
<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>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nie OCA], [https://pdbe.org/1nie PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nie RCSB], [https://www.ebi.ac.uk/pdbsum/1nie PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nie ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nie OCA], [http://www.ebi.ac.uk/pdbsum/1nie PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nie RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/NIR_ACHCY NIR_ACHCY]
 +
== 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/ni/1nie_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=1nie ConSurf].
 +
<div style="clear:both"></div>
-
'''THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES, WITH NITRITE BOUND AND WITH TYPE II CU DEPLETED'''
+
==See Also==
-
 
+
*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
High resolution x-ray crystallographic structures of nitrite reductase from Achromobacter cycloclastes, undertaken in order to understand the pH optimum of the reaction with nitrite, show that at pH 5.0, 5.4, 6.0, 6.2, and 6.8, no significant changes occur, other than in the occupancy of the type II copper at the active site. An extensive network of hydrogen bonds, both within and between subunits of the trimer, maintains the rigidity of the protein structure. A water occupies a site approximately 1.5 A from the site of the type II copper in the structure of the type II copper-depleted structure (at pH 5.4), again with no other significant changes in structure. In nitrite-soaked crystals, nitrite binds via its oxygens to the type II copper and replaces the water normally bound to the type II copper. The active-site cavity of the protein is distinctly hydrophobic on one side and hydrophilic on the other, providing a possible path for diffusion of the product NO. Asp-98 exhibits thermal parameter values higher than its surroundings, suggesting a role in shuttling the two protons necessary for the overall reaction. The strong structural homology with cupredoxins is described.
+
-
 
+
-
==About this Structure==
+
-
1NIE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIE OCA].
+
-
 
+
-
==Reference==
+
-
The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2- bound and with type II copper depleted., Adman ET, Godden JW, Turley S, J Biol Chem. 1995 Nov 17;270(46):27458-74. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7499203 7499203]
+
[[Category: Achromobacter cycloclastes]]
[[Category: Achromobacter cycloclastes]]
-
[[Category: Nitrite reductase (NO-forming)]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Adman ET]]
-
[[Category: Adman, E T.]]
+
[[Category: Godden JW]]
-
[[Category: Godden, J W.]]
+
[[Category: Turley S]]
-
[[Category: Turley, S.]]
+
-
[[Category: oxidoreductase (nitric oxide(a))]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:30:50 2008''
+

Current revision

THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES, WITH NITRITE BOUND AND WITH TYPE II CU DEPLETED

PDB ID 1nie

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1nie"
Personal tools