2nyb
From Proteopedia
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| - | [[Image:2nyb.gif|left|200px]] | + | [[Image:2nyb.gif|left|200px]] |
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| - | '''Crystal structure of E.Coli Iron Superoxide Dismutase Q69E at 1.1 Angstrom resolution''' | + | {{Structure |
| + | |PDB= 2nyb |SIZE=350|CAPTION= <scene name='initialview01'>2nyb</scene>, resolution 1.100Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene> and <scene name='pdbligand=O:OXYGEN ATOM'>O</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] | ||
| + | |GENE= sodB, b1656, JW1648 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | }} | ||
| + | |||
| + | '''Crystal structure of E.Coli Iron Superoxide Dismutase Q69E at 1.1 Angstrom resolution''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2NYB is a [ | + | 2NYB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NYB OCA]. |
==Reference== | ==Reference== | ||
| - | How can a single second sphere amino acid substitution cause reduction midpoint potential changes of hundreds of millivolts?, Yikilmaz E, Porta J, Grove LE, Vahedi-Faridi A, Bronshteyn Y, Brunold TC, Borgstahl GE, Miller AF, J Am Chem Soc. 2007 Aug 15;129(32):9927-40. Epub 2007 Jul 12. PMID:[http:// | + | How can a single second sphere amino acid substitution cause reduction midpoint potential changes of hundreds of millivolts?, Yikilmaz E, Porta J, Grove LE, Vahedi-Faridi A, Bronshteyn Y, Brunold TC, Borgstahl GE, Miller AF, J Am Chem Soc. 2007 Aug 15;129(32):9927-40. Epub 2007 Jul 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17628062 17628062] |
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: iron superoxide dismutase q69e]] | [[Category: iron superoxide dismutase q69e]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:52:44 2008'' |
Revision as of 15:52, 20 March 2008
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| , resolution 1.100Å | |||||||
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| Ligands: | and | ||||||
| Gene: | sodB, b1656, JW1648 (Escherichia coli) | ||||||
| Activity: | Superoxide dismutase, with EC number 1.15.1.1 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of E.Coli Iron Superoxide Dismutase Q69E at 1.1 Angstrom resolution
Overview
The active site metal ion of superoxide dismutase (SOD) is reduced and reoxidized as it disproportionates superoxide to dioxygen and hydrogen peroxide. Thus, the reduction midpoint potential (Em) is a critical determinant of catalytic activity. In E. coli Fe-containing SOD (FeSOD), reduction of Fe3+ is accompanied by protonation of a coordinated OH-, to produce Fe2+ coordinated by H2O. The coordinated solvent's only contact with the protein beyond the active site is a conserved Gln residue. Mutation of this Gln to His or Glu resulted in elevation of the Em by 220 mV and more than 660 mV, respectively [Yikilmaz et al., Biochemistry 2006, 45, 1151-1161], despite the fact that overall protein structure was preserved, His is a chemically conservative replacement for Gln, and neutral Glu is isostructural and isoelectronic with Gln. Therefore, we have investigated several possible bases for the elevated Em's, including altered Fe electronic structure, altered active site electrostatics, altered H-bonding and altered redox-coupled proton transfer. Using EPR, MCD, and NMR spectroscopies, we find that the active site electronic structures of the two mutants resemble that of the WT enzyme, for both oxidation states, and Q69E-FeSOD's apparent deviation from WT-like Fe3+ coordination in the oxidized state can be explained by increased affinity for a small anion. Spontaneous coordination of an exogenous anion can only stabilize oxidized Q69E-Fe3+SOD and, therefore, cannot account for the increased Em of Q69E FeSOD. WT-like anion binding affinities and active site pK's indicate that His69 of Q69H-FeSOD is neutral in both oxidation states, like Gln69 of WT-FeSOD, whereas Glu69 appears to be neutral in the oxidized state but ionized in the reduced state of Q69E-FeSOD. A 1.1 A resolution crystal structure of Q69E-Fe2+SOD indicates that Glu69 accepts a strong H-bond from coordinated solvent in the reduced state, in contrast to the case in WT-FeSOD where Gln69 donates an H-bond. These data and DFT calculations lead to the proposal that the elevated Em of Q69E-FeSOD can be substantially explained by (1) relief from enforced H-bond donation in the reduced state, (2) Glu69's capacity to provide a proton for proton-coupled Fe3+ reduction, and (3) strong hydrogen bond acceptance in the reduced state, which stabilizes coordinated H2O. Our results thus support the hypothesis that the protein matrix can apply significant redox tuning via its influence over redox-coupled proton transfer and the energy associated with it.
About this Structure
2NYB is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
How can a single second sphere amino acid substitution cause reduction midpoint potential changes of hundreds of millivolts?, Yikilmaz E, Porta J, Grove LE, Vahedi-Faridi A, Bronshteyn Y, Brunold TC, Borgstahl GE, Miller AF, J Am Chem Soc. 2007 Aug 15;129(32):9927-40. Epub 2007 Jul 12. PMID:17628062
Page seeded by OCA on Thu Mar 20 17:52:44 2008
