1yfd: Difference between revisions
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'''Crystal structure of the Y122H mutant of ribonucleotide reductase R2 protein from E. coli''' | {{Structure | ||
|PDB= 1yfd |SIZE=350|CAPTION= <scene name='initialview01'>1yfd</scene>, resolution 1.90Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene> and <scene name='pdbligand=F2O:MU-OXO-DIIRON(III)'>F2O</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] | |||
|GENE= nrdB, ftsB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |||
}} | |||
'''Crystal structure of the Y122H mutant of ribonucleotide reductase R2 protein from E. coli''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1YFD is a [ | 1YFD 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=1YFD OCA]. | ||
==Reference== | ==Reference== | ||
A new tyrosyl radical on Phe208 as ligand to the diiron center in Escherichia coli ribonucleotide reductase, mutant R2-Y122H. Combined x-ray diffraction and EPR/ENDOR studies., Kolberg M, Logan DT, Bleifuss G, Potsch S, Sjoberg BM, Graslund A, Lubitz W, Lassmann G, Lendzian F, J Biol Chem. 2005 Mar 25;280(12):11233-46. Epub 2005 Jan 5. PMID:[http:// | A new tyrosyl radical on Phe208 as ligand to the diiron center in Escherichia coli ribonucleotide reductase, mutant R2-Y122H. Combined x-ray diffraction and EPR/ENDOR studies., Kolberg M, Logan DT, Bleifuss G, Potsch S, Sjoberg BM, Graslund A, Lubitz W, Lassmann G, Lendzian F, J Biol Chem. 2005 Mar 25;280(12):11233-46. Epub 2005 Jan 5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15634667 15634667] | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Ribonucleoside-diphosphate reductase]] | [[Category: Ribonucleoside-diphosphate reductase]] | ||
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[[Category: di-iron center]] | [[Category: di-iron center]] | ||
''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 15:22:08 2008'' | ||
Revision as of 16:22, 20 March 2008
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| , resolution 1.90Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | and | ||||||
| Gene: | nrdB, ftsB (Escherichia coli) | ||||||
| Activity: | Ribonucleoside-diphosphate reductase, with EC number 1.17.4.1 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of the Y122H mutant of ribonucleotide reductase R2 protein from E. coli
OverviewOverview
The R2 protein subunit of class I ribonucleotide reductase (RNR) belongs to a structurally related family of oxygen bridged diiron proteins. In wild-type R2 of Escherichia coli, reductive cleavage of molecular oxygen by the diferrous iron center generates a radical on a nearby tyrosine residue (Tyr122), which is essential for the enzymatic activity of RNR, converting ribonucleotides into deoxyribonucleotides. In this work, we characterize the mutant E. coli protein R2-Y122H, where the radical site is substituted with a histidine residue. The x-ray structure verifies the mutation. R2-Y122H contains a novel stable paramagnetic center which we name H, and which we have previously proposed to be a diferric iron center with a strongly coupled radical, Fe(III)Fe(III)R.. Here we report a detailed characterization of center H, using 1H/2H -14N/15N- and 57Fe-ENDOR in comparison with the Fe(III)Fe(IV) intermediate X observed in the iron reconstitution reaction of R2. Specific deuterium labeling of phenylalanine residues reveals that the radical results from a phenylalanine. As Phe208 is the only phenylalanine in the ligand sphere of the iron site, and generation of a phenyl radical requires a very high oxidation potential, we propose that in Y122H residue Phe208 is hydroxylated, as observed earlier in another mutant (R2-Y122F/E238A), and further oxidized to a phenoxyl radical, which is coordinated to Fe1. This work demonstrates that small structural changes can redirect the reactivity of the diiron site, leading to oxygenation of a hydrocarbon, as observed in the structurally similar methane monoxygenase, and beyond, to formation of a stable iron-coordinated radical.
About this StructureAbout this Structure
1YFD is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
ReferenceReference
A new tyrosyl radical on Phe208 as ligand to the diiron center in Escherichia coli ribonucleotide reductase, mutant R2-Y122H. Combined x-ray diffraction and EPR/ENDOR studies., Kolberg M, Logan DT, Bleifuss G, Potsch S, Sjoberg BM, Graslund A, Lubitz W, Lassmann G, Lendzian F, J Biol Chem. 2005 Mar 25;280(12):11233-46. Epub 2005 Jan 5. PMID:15634667
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