1e2r: Difference between revisions
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|PDB= 1e2r |SIZE=350|CAPTION= <scene name='initialview01'>1e2r</scene>, resolution 1.59Å | |PDB= 1e2r |SIZE=350|CAPTION= <scene name='initialview01'>1e2r</scene>, resolution 1.59Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=DHE:HEME+D'>DHE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1e2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e2r OCA], [http://www.ebi.ac.uk/pdbsum/1e2r PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1e2r RCSB]</span> | |||
}} | }} | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Fulop, V.]] | [[Category: Fulop, V.]] | ||
[[Category: cyanide]] | [[Category: cyanide]] | ||
[[Category: denitrification]] | [[Category: denitrification]] | ||
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[[Category: periplasmic]] | [[Category: periplasmic]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:53:55 2008'' | ||
Revision as of 19:53, 30 March 2008
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| , resolution 1.59Å | |||||||
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| Ligands: | , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED AND CYANIDE BOUND
OverviewOverview
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.
About this StructureAbout this Structure
1E2R is a Single protein structure of sequence from Paracoccus denitrificans. Full crystallographic information is available from OCA.
ReferenceReference
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
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