2cvs
From Proteopedia
(New page: 200px<br /><applet load="2cvs" size="450" color="white" frame="true" align="right" spinBox="true" caption="2cvs, resolution 2.60Å" /> '''Structures of Yeast ...) |
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| - | [[Image:2cvs.gif|left|200px]]<br /><applet load="2cvs" size=" | + | [[Image:2cvs.gif|left|200px]]<br /><applet load="2cvs" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2cvs, resolution 2.60Å" /> | caption="2cvs, resolution 2.60Å" /> | ||
'''Structures of Yeast Ribonucleotide Reductase I'''<br /> | '''Structures of Yeast Ribonucleotide Reductase I'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Ribonucleotide reductase catalyzes a crucial step in de novo DNA synthesis | + | Ribonucleotide reductase catalyzes a crucial step in de novo DNA synthesis and is allosterically controlled by relative levels of dNTPs to maintain a balanced pool of deoxynucleoside triphosphates in the cell. In eukaryotes, the enzyme comprises a heterooligomer of alpha(2) and beta(2) subunits. The alpha subunit, Rnr1, contains catalytic and regulatory sites. Here, we report the only x-ray structures of the eukaryotic alpha subunit of ribonucleotide reductase from Saccharomyces cerevisiae. The structures of the apo-, AMPPNP only-, AMPPNP-CDP-, AMPPNP-UDP-, dGTP-ADP- and TTP-GDP-bound complexes give insight into substrate and effector binding and specificity cross-talk. These are Class I structures with the only fully ordered catalytic sites, including loop 2, a stretch of polypeptide that spans specificity and catalytic sites, conferring specificity. Binding of specificity effector rearranges loop 2; in our structures, this rearrangement moves P294, a residue unique to eukaryotes, out of the catalytic site, accommodating substrate binding. Substrate binding further rearranges loop 2. Cross-talk, by which effector binding regulates substrate preference, occurs largely through R293 and Q288 of loop 2, which are analogous to residues in Thermotoga maritima that mediate cross-talk. However loop-2 conformations and residue-substrate interactions differ substantially between yeast and T. maritima. In most effector-substrate complexes, water molecules help mediate substrate-loop 2 interactions. Finally, the substrate ribose binds with its 3' hydroxyl closer than its 2' hydroxyl to C218 of the catalytic redox pair. We also see a conserved water molecule at the catalytic site in all our structures, near the ribose 2' hydroxyl. |
==About this Structure== | ==About this Structure== | ||
| - | 2CVS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Active as [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] Full crystallographic information is available from [http:// | + | 2CVS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CVS OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Dealwis, C.]] | [[Category: Dealwis, C.]] | ||
[[Category: Faber, C.]] | [[Category: Faber, C.]] | ||
| - | [[Category: Fairman, J | + | [[Category: Fairman, J W.]] |
[[Category: Racca, J.]] | [[Category: Racca, J.]] | ||
[[Category: Uchiki, T.]] | [[Category: Uchiki, T.]] | ||
| Line 24: | Line 24: | ||
[[Category: ribonucleotide reductase]] | [[Category: ribonucleotide reductase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:53:00 2008'' |
Revision as of 14:53, 21 February 2008
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Structures of Yeast Ribonucleotide Reductase I
Overview
Ribonucleotide reductase catalyzes a crucial step in de novo DNA synthesis and is allosterically controlled by relative levels of dNTPs to maintain a balanced pool of deoxynucleoside triphosphates in the cell. In eukaryotes, the enzyme comprises a heterooligomer of alpha(2) and beta(2) subunits. The alpha subunit, Rnr1, contains catalytic and regulatory sites. Here, we report the only x-ray structures of the eukaryotic alpha subunit of ribonucleotide reductase from Saccharomyces cerevisiae. The structures of the apo-, AMPPNP only-, AMPPNP-CDP-, AMPPNP-UDP-, dGTP-ADP- and TTP-GDP-bound complexes give insight into substrate and effector binding and specificity cross-talk. These are Class I structures with the only fully ordered catalytic sites, including loop 2, a stretch of polypeptide that spans specificity and catalytic sites, conferring specificity. Binding of specificity effector rearranges loop 2; in our structures, this rearrangement moves P294, a residue unique to eukaryotes, out of the catalytic site, accommodating substrate binding. Substrate binding further rearranges loop 2. Cross-talk, by which effector binding regulates substrate preference, occurs largely through R293 and Q288 of loop 2, which are analogous to residues in Thermotoga maritima that mediate cross-talk. However loop-2 conformations and residue-substrate interactions differ substantially between yeast and T. maritima. In most effector-substrate complexes, water molecules help mediate substrate-loop 2 interactions. Finally, the substrate ribose binds with its 3' hydroxyl closer than its 2' hydroxyl to C218 of the catalytic redox pair. We also see a conserved water molecule at the catalytic site in all our structures, near the ribose 2' hydroxyl.
About this Structure
2CVS is a Single protein structure of sequence from Saccharomyces cerevisiae. Active as Ribonucleoside-diphosphate reductase, with EC number 1.17.4.1 Full crystallographic information is available from OCA.
Reference
Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation., Xu H, Faber C, Uchiki T, Fairman JW, Racca J, Dealwis C, Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4022-7. Epub 2006 Mar 6. PMID:16537479
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