2cvw: Difference between revisions
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|PDB= 2cvw |SIZE=350|CAPTION= <scene name='initialview01'>2cvw</scene>, resolution 2.40Å | |PDB= 2cvw |SIZE=350|CAPTION= <scene name='initialview01'>2cvw</scene>, resolution 2.40Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=GDP:GUANOSINE-5'-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5'-TRIPHOSPHATE'>TTP</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] | |ACTIVITY= <span class='plainlinks'>[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] </span> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1zyz|1ZYZ]], [[2cvs|2CVS]], [[2cvt|2CVT]], [[2cvu|2CVU]], [[2cvv|2CVV]], [[2cvx|2CVX]], [[2cvy|2CVY]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cvw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvw OCA], [http://www.ebi.ac.uk/pdbsum/2cvw PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2cvw RCSB]</span> | |||
}} | }} | ||
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[[Category: Uchiki, T.]] | [[Category: Uchiki, T.]] | ||
[[Category: Xu, H.]] | [[Category: Xu, H.]] | ||
[[Category: dntp regulation]] | [[Category: dntp regulation]] | ||
[[Category: eukaryotic]] | [[Category: eukaryotic]] | ||
[[Category: ribonucleotide reductase]] | [[Category: ribonucleotide reductase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:27:01 2008'' | ||
Revision as of 02:27, 31 March 2008
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| , resolution 2.40Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Activity: | Ribonucleoside-diphosphate reductase, with EC number 1.17.4.1 | ||||||
| Related: | 1ZYZ, 2CVS, 2CVT, 2CVU, 2CVV, 2CVX, 2CVY
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structures of Yeast Ribonucleotide Reductase I
OverviewOverview
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 StructureAbout this Structure
2CVW is a Single protein structure of sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA.
ReferenceReference
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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