1qyb
From Proteopedia
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|PDB= 1qyb |SIZE=350|CAPTION= <scene name='initialview01'>1qyb</scene>, resolution 1.75Å | |PDB= 1qyb |SIZE=350|CAPTION= <scene name='initialview01'>1qyb</scene>, resolution 1.75Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= RR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=881 Desulfovibrio vulgaris]) | |GENE= RR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=881 Desulfovibrio vulgaris]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1lkm|1LKM]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qyb OCA], [http://www.ebi.ac.uk/pdbsum/1qyb PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1qyb RCSB]</span> | ||
}} | }} | ||
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[[Category: Rose, J.]] | [[Category: Rose, J.]] | ||
[[Category: Wang, B C.]] | [[Category: Wang, B C.]] | ||
| - | [[Category: FE]] | ||
| - | [[Category: SO4]] | ||
| - | [[Category: ZN]] | ||
[[Category: diiron four-helix bundle]] | [[Category: diiron four-helix bundle]] | ||
[[Category: rubredoxin-like]] | [[Category: rubredoxin-like]] | ||
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[[Category: zinc-substituted]] | [[Category: zinc-substituted]] | ||
| - | ''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 23:20:40 2008'' |
Revision as of 20:20, 30 March 2008
| |||||||
| , resolution 1.75Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | RR (Desulfovibrio vulgaris) | ||||||
| Related: | 1LKM
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
X-ray crystal structure of Desulfovibrio vulgaris rubrerythrin with zinc substituted into the [Fe(SCys)4] site and alternative diiron site structures
Overview
The X-ray crystal structure of recombinant Desulfovibrio vulgaris rubrerythrin (Rbr) that was subjected to metal constitution first with zinc and then iron, yielding ZnS(4)Rbr, is reported. A [Zn(SCys)(4)] site with no iron and a diiron site with no appreciable zinc in ZnS(4)Rbr were confirmed by analysis of the anomalous scattering data. Partial reduction of the diiron site occurred during the synchrotron X-ray irradiation at 95 K, resulting in two different diiron site structures in the ZnS(4)Rbr crystal. These two structures can be classified as containing mixed-valent Fe1(III)(mu-OH(-))(mu-GluCO(2)(-))(2)Fe2(II) and Fe1(II)(mu-GluCO(2)(-))(2)Fe2(III)-OH(-) cores. The data do not show any evidence for alternative positions of the protein or solvent ligands. The iron and ligand positions of the solvent-bridged site are close to those of the diferric site in all-iron Rbr. The diiron site with only the two carboxylato bridges differs by an approximately 2 A shift in the position of Fe1, which changes from six- to four-coordination. The Fe1- - -Fe2 distance (3.6 A) in this latter site is significantly longer than that of the site with the additional solvent bridge (3.4 A) but significantly shorter than that previously reported for the diferrous site (4.0 A) in all-iron Rbr. The apparent redox-induced movement of Fe1 at 95 K in the ZnS(4)Rbr crystal implies an extremely low activation barrier, which is consistent with the rapid (approximately 30 s(-1)) room temperature turnover of the all-iron Rbr during its catalysis of two-electron reduction of hydrogen peroxide. ZnS(4)Rbr does not show peroxidase activity, presumably because the [Zn(SCys)(4)] site, unlike the [Fe(SCys)(4)] site, cannot mediate electron transfer to the diiron site. One or both of the diiron site structures in the cryoreduced ZnS(4)Rbr crystal are likely to represent that (those) of transient mixed-valent diiron site(s) that must occur upon return of the diferric to the diferrous oxidation level during peroxidase turnover.
About this Structure
1QYB is a Single protein structure of sequence from Desulfovibrio vulgaris. Full crystallographic information is available from OCA.
Reference
X-ray crystal structure of Desulfovibrio vulgaris rubrerythrin with zinc substituted into the [Fe(SCys)4] site and alternative diiron site structures., Jin S, Kurtz DM Jr, Liu ZJ, Rose J, Wang BC, Biochemistry. 2004 Mar 23;43(11):3204-13. PMID:15023070
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