1kcb

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:16, 25 October 2023) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1kcb.gif|left|200px]]
 
-
{{Structure
+
==Crystal Structure of a NO-forming Nitrite Reductase Mutant: an Analog of a Transition State in Enzymatic Reaction==
-
|PDB= 1kcb |SIZE=350|CAPTION= <scene name='initialview01'>1kcb</scene>, resolution 1.65&Aring;
+
<StructureSection load='1kcb' size='340' side='right'caption='[[1kcb]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=CU:COPPER (II) ION'>CU</scene>
+
<table><tr><td colspan='2'>[[1kcb]] 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=1KCB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KCB FirstGlance]. <br>
-
|ACTIVITY= [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]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#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>
-
}}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kcb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kcb OCA], [https://pdbe.org/1kcb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kcb RCSB], [https://www.ebi.ac.uk/pdbsum/1kcb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kcb ProSAT]</span></td></tr>
 +
</table>
 +
== 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/kc/1kcb_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=1kcb ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
I257E was obtained by site directed mutagenesis of nitrite reductase from Achromobacter cycloclastes. The mutant has no enzyme activity. Its crystal structure determined at 1.65A resolution shows that the side-chain carboxyl group of the mutated residue, Glu257, coordinates with the type 2 copper in the mutant and blocks the contact between the type 2 copper and its solvent channel, indicating that the accessibility of the type 2 copper is essential for maintaining the activity of nitrite reductase. The carboxylate is an analog of the substrate, nitrite, but the distances between the type 2 copper and the two oxygen atoms of the side-chain carboxyl group are reversed in comparison to the binding of nitrite to the native enzyme. In the mutant, both the type 2 copper and the N epsilon atom on the imidazole ring of its coordinated residue His135 move in the substrate binding direction relative to the native enzyme. In addition, an EPR study showed that the type 2 copper in the mutant is in a reduced state. We propose that mutant I257E is in a state corresponding to a transition state in the enzymatic reaction.
-
'''Crystal Structure of a NO-forming Nitrite Reductase Mutant: an Analog of a Transition State in Enzymatic Reaction'''
+
Crystal structure of a NO-forming nitrite reductase mutant: an analog of a transition state in enzymatic reaction.,Liu SQ, Chang T, Liu MY, LeGall J, Chang WC, Zhang JP, Liang DC, Chang WR Biochem Biophys Res Commun. 2003 Mar 14;302(3):568-74. PMID:12615072<ref>PMID:12615072</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1kcb" style="background-color:#fffaf0;"></div>
-
==Overview==
+
==See Also==
-
I257E was obtained by site directed mutagenesis of nitrite reductase from Achromobacter cycloclastes. The mutant has no enzyme activity. Its crystal structure determined at 1.65A resolution shows that the side-chain carboxyl group of the mutated residue, Glu257, coordinates with the type 2 copper in the mutant and blocks the contact between the type 2 copper and its solvent channel, indicating that the accessibility of the type 2 copper is essential for maintaining the activity of nitrite reductase. The carboxylate is an analog of the substrate, nitrite, but the distances between the type 2 copper and the two oxygen atoms of the side-chain carboxyl group are reversed in comparison to the binding of nitrite to the native enzyme. In the mutant, both the type 2 copper and the N epsilon atom on the imidazole ring of its coordinated residue His135 move in the substrate binding direction relative to the native enzyme. In addition, an EPR study showed that the type 2 copper in the mutant is in a reduced state. We propose that mutant I257E is in a state corresponding to a transition state in the enzymatic reaction.
+
*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
-
 
+
== References ==
-
==About this Structure==
+
<references/>
-
1KCB 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=1KCB OCA].
+
__TOC__
-
 
+
</StructureSection>
-
==Reference==
+
-
Crystal structure of a NO-forming nitrite reductase mutant: an analog of a transition state in enzymatic reaction., Liu SQ, Chang T, Liu MY, LeGall J, Chang WC, Zhang JP, Liang DC, Chang WR, Biochem Biophys Res Commun. 2003 Mar 14;302(3):568-74. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12615072 12615072]
+
[[Category: Achromobacter cycloclastes]]
[[Category: Achromobacter cycloclastes]]
-
[[Category: Nitrite reductase (NO-forming)]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Chang T]]
-
[[Category: Chang, T.]]
+
[[Category: Chang WC]]
-
[[Category: Chang, W C.]]
+
[[Category: Chang WR]]
-
[[Category: Chang, W R.]]
+
[[Category: LeGall J]]
-
[[Category: LeGall, J.]]
+
[[Category: Liang DC]]
-
[[Category: Liang, D C.]]
+
[[Category: Liu MY]]
-
[[Category: Liu, M Y.]]
+
[[Category: Liu SQ]]
-
[[Category: Liu, S Q.]]
+
[[Category: Zhang JP]]
-
[[Category: Zhang, J P.]]
+
-
[[Category: CU]]
+
-
[[Category: beta barrel]]
+
-
[[Category: copper-containing nitrite reductase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:15:27 2008''
+

Current revision

Crystal Structure of a NO-forming Nitrite Reductase Mutant: an Analog of a Transition State in Enzymatic Reaction

PDB ID 1kcb

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/1kcb"
Personal tools