2cyp
From Proteopedia
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|PDB= 2cyp |SIZE=350|CAPTION= <scene name='initialview01'>2cyp</scene>, resolution 1.7Å | |PDB= 2cyp |SIZE=350|CAPTION= <scene name='initialview01'>2cyp</scene>, resolution 1.7Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene> | + | |LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cyp OCA], [http://www.ebi.ac.uk/pdbsum/2cyp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2cyp RCSB]</span> | ||
}} | }} | ||
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[[Category: Kraut, J.]] | [[Category: Kraut, J.]] | ||
[[Category: Poulos, T L.]] | [[Category: Poulos, T L.]] | ||
| - | [[Category: HEM]] | ||
| - | [[Category: O]] | ||
[[Category: oxidoreductase (h2o2(a))]] | [[Category: oxidoreductase (h2o2(a))]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:28:09 2008'' |
Revision as of 23:28, 30 March 2008
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| , resolution 1.7Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Activity: | Cytochrome-c peroxidase, with EC number 1.11.1.5 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of yeast cytochrome C peroxidase refined at 1.7-angstroms resolution
Overview
The crystal structure of cytochrome c peroxidase (EC 1.11.1.5) has been refined to an R factor of 0.20 computed for all reflections to 1.7 A. The refined molecular model includes 263 bound water molecules and allows for x-ray scattering by amorphous solvent. The mean positional error in atomic coordinates is estimated to lie between 0.12 and 0.21 A. Two factors are identified which may account for the ability of the enzyme to stabilize high-oxidation states of the heme iron during catalysis: 1) the proximal histidine forms a hydrogen bond with a buried aspartic acid side chain, Asp-235; and 2) the heme environment is more polar than in the cytochromes c or globins, owing to the presence of the partially buried side-chain of Arg-48 and five water molecules bound in close proximity to the heme. Two of these occupy the presumed peroxide-binding site. Two candidates are likely for the side chain that is oxidized to a free radical during formation of Compound I: 1) Trp-51, which rests 3.3 A above the heme plane in close proximity (2.7 A) to the sixth coordination position; and 2) Met-172, which is 3.7 A from the heme. Nucleophilic stabilization of the methionyl cation radical may be possible via Asp-235. His-181 is found to lie coplanar with the heme in a niche between the two propionates near the suspected cytochrome c-binding site. A network of hydrogen bonds involving this histidine may provide a preferred pathway for electron transfer between hemes.
About this Structure
2CYP is a Single protein structure of sequence from Saccharomyces cerevisiae. This structure supersedes the now removed PDB entry 1CYP. Full crystallographic information is available from OCA.
Reference
Crystal structure of yeast cytochrome c peroxidase refined at 1.7-A resolution., Finzel BC, Poulos TL, Kraut J, J Biol Chem. 1984 Nov 10;259(21):13027-36. PMID:6092361
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