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[[Image:1e2r.gif|left|200px]]


{{Structure
==CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED AND CYANIDE BOUND==
|PDB= 1e2r |SIZE=350|CAPTION= <scene name='initialview01'>1e2r</scene>, resolution 1.59&Aring;
<StructureSection load='1e2r' size='340' side='right'caption='[[1e2r]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=DHE:HEME+D'>DHE</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
<table><tr><td colspan='2'>[[1e2r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E2R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E2R FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.59&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</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=1e2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e2r OCA], [https://pdbe.org/1e2r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e2r RCSB], [https://www.ebi.ac.uk/pdbsum/1e2r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e2r ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NIRS_PARPN NIRS_PARPN]
== 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/e2/1e2r_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1e2r ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We present a 1.59-A resolution crystal structure of reduced Paracoccus pantotrophus cytochrome cd(1) with cyanide bound to the d(1) heme and His/Met coordination of the c heme. Fe-C-N bond angles are 146 degrees for the A subunit and 164 degrees for the B subunit of the dimer. The nitrogen atom of bound cyanide is within hydrogen bonding distance of His(345) and His(388) and either a water molecule in subunit A or Tyr(25) in subunit B. The ferrous heme-cyanide complex is unusually stable (K(d) approximately 10(-6) m); we propose that this reflects both the design of the specialized d(1) heme ring and a general feature of anion reductases with active site heme. Oxidation of crystals of reduced, cyanide-bound, cytochrome cd(1) results in loss of cyanide and return to the native structure with Tyr(25) as a ligand to the d(1) heme iron and switching to His/His coordination at the c-type heme. No reason for unusually weak binding of cyanide to the ferric state can be identified; rather it is argued that the protein is designed such that a chelate-based effect drives displacement by tyrosine of cyanide or a weaker ligand, like reaction product nitric oxide, from the ferric d(1) heme.


'''CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED AND CYANIDE BOUND'''
X-ray crystallographic study of cyanide binding provides insights into the structure-function relationship for cytochrome cd1 nitrite reductase from Paracoccus pantotrophus.,Jafferji A, Allen JW, Ferguson SJ, Fulop V J Biol Chem. 2000 Aug 18;275(33):25089-94. PMID:10827177<ref>PMID:10827177</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1e2r" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
We present a 1.59-A resolution crystal structure of reduced Paracoccus pantotrophus cytochrome cd(1) with cyanide bound to the d(1) heme and His/Met coordination of the c heme. Fe-C-N bond angles are 146 degrees for the A subunit and 164 degrees for the B subunit of the dimer. The nitrogen atom of bound cyanide is within hydrogen bonding distance of His(345) and His(388) and either a water molecule in subunit A or Tyr(25) in subunit B. The ferrous heme-cyanide complex is unusually stable (K(d) approximately 10(-6) m); we propose that this reflects both the design of the specialized d(1) heme ring and a general feature of anion reductases with active site heme. Oxidation of crystals of reduced, cyanide-bound, cytochrome cd(1) results in loss of cyanide and return to the native structure with Tyr(25) as a ligand to the d(1) heme iron and switching to His/His coordination at the c-type heme. No reason for unusually weak binding of cyanide to the ferric state can be identified; rather it is argued that the protein is designed such that a chelate-based effect drives displacement by tyrosine of cyanide or a weaker ligand, like reaction product nitric oxide, from the ferric d(1) heme.
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
 
*[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]]
==About this Structure==
== References ==
1E2R is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E2R OCA].
<references/>
 
__TOC__
==Reference==
</StructureSection>
X-ray crystallographic study of cyanide binding provides insights into the structure-function relationship for cytochrome cd1 nitrite reductase from Paracoccus pantotrophus., Jafferji A, Allen JW, Ferguson SJ, Fulop V, J Biol Chem. 2000 Aug 18;275(33):25089-94. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10827177 10827177]
[[Category: Large Structures]]
[[Category: Paracoccus denitrificans]]
[[Category: Paracoccus denitrificans]]
[[Category: Single protein]]
[[Category: Fulop V]]
[[Category: Fulop, V.]]
[[Category: CYN]]
[[Category: DHE]]
[[Category: GOL]]
[[Category: HEC]]
[[Category: cyanide]]
[[Category: denitrification]]
[[Category: electron transport]]
[[Category: enzyme]]
[[Category: nitrite reductase]]
[[Category: oxidoreductase]]
[[Category: periplasmic]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:48:36 2008''

Latest revision as of 07:14, 9 October 2024

CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED AND CYANIDE BOUND

1e2r, resolution 1.59Å

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