1j2c
From Proteopedia
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|PDB= 1j2c |SIZE=350|CAPTION= <scene name='initialview01'>1j2c</scene>, resolution 2.4Å | |PDB= 1j2c |SIZE=350|CAPTION= <scene name='initialview01'>1j2c</scene>, resolution 2.4Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1j2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j2c OCA], [http://www.ebi.ac.uk/pdbsum/1j2c PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1j2c RCSB]</span> | ||
}} | }} | ||
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[[Category: Sakamoto, H.]] | [[Category: Sakamoto, H.]] | ||
[[Category: Sugishima, M.]] | [[Category: Sugishima, M.]] | ||
| - | [[Category: BLA]] | ||
| - | [[Category: FE]] | ||
[[Category: bent helix]] | [[Category: bent helix]] | ||
[[Category: enzyme-product complex]] | [[Category: enzyme-product complex]] | ||
| - | ''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 21:27:53 2008'' |
Revision as of 18:27, 30 March 2008
| |||||||
| , resolution 2.4Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Activity: | Heme oxygenase, with EC number 1.14.99.3 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of rat heme oxygenase-1 in complex with biliverdin IXalpha-iron cluster
Overview
The crystal structure of rat heme oxygenase-1 in complex with biliverdin-iron chelate (biliverdin(Fe)-HO-1), the immediate precursor of the final product, biliverdin, has been determined at a 2.4-A resolution. The electron density in the heme pocket clearly showed that the tetrapyrrole ring of heme is cleaved at the alpha-meso edge. Like the heme bound to HO-1, biliverdin-iron chelate is located between the distal and proximal helices, but its accommodation state seems to be less stable in light of the disordering of the solvent-exposed propionate and vinyl groups. The middle of the distal helix is shifted away from the center of the active site in biliverdin(Fe)-HO-1, increasing the size of the heme pocket. The hydrogen-bonding interaction between Glu-29 and Gln-38, considered to restrain the orientation of the proximal helix in the heme-HO-1 complex, was lost in biliverdin(Fe)-HO-1, leading to relaxation of the helix. Biliverdin has a distorted helical conformation; the lactam oxygen atom of its pyrrole ring-A interacted with Asp-140 through a hydrogen-bonding solvent network. Because of the absence of a distal water ligand, the iron atom is five-coordinated with His-25 and four pyrrole nitrogen atoms. The coordination geometry deviates considerably from a square pyramid, suggesting that the iron may be readily dissociated. We speculate that the opened conformation of the heme pocket facilitates sequential product release, first iron then biliverdin, and that because of biliverdin's increased flexibility, iron release triggers its slow dissociation.
About this Structure
1J2C is a Single protein structure of sequence from Rattus norvegicus. Full crystallographic information is available from OCA.
Reference
Crystal structure of rat heme oxygenase-1 in complex with biliverdin-iron chelate. Conformational change of the distal helix during the heme cleavage reaction., Sugishima M, Sakamoto H, Higashimoto Y, Noguchi M, Fukuyama K, J Biol Chem. 2003 Aug 22;278(34):32352-8. Epub 2003 Jun 6. PMID:12794075
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