Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase.
Journal, issue, pages	Structure, Vol. 20, Issue 8, Page 1374-1383, Year 2012
Publish date	Aug 8, 2012
Authors	Christina M Zimanyi / Nozomi Ando / Edward J Brignole / Francisco J Asturias / Joanne Stubbe / Catherine L Drennan /
PubMed Abstract	Ribonucleotide reductases (RNRs) provide the precursors for DNA biosynthesis and repair and are successful targets for anticancer drugs such as clofarabine and gemcitabine. Recently, we reported that ...Ribonucleotide reductases (RNRs) provide the precursors for DNA biosynthesis and repair and are successful targets for anticancer drugs such as clofarabine and gemcitabine. Recently, we reported that dATP inhibits E. coli class Ia RNR by driving formation of RNR subunits into α4β4 rings. Here, we present the first X-ray structure of a gemcitabine-inhibited E. coli RNR and show that the previously described α4β4 rings can interlock to form an unprecedented (α4β4)2 megacomplex. This complex is also seen in a higher-resolution dATP-inhibited RNR structure presented here, which employs a distinct crystal lattice from that observed in the gemcitabine-inhibited case. With few reported examples of protein catenanes, we use data from small-angle X-ray scattering and electron microscopy to both understand the solution conditions that contribute to concatenation in RNRs as well as present a mechanism for the formation of these unusual structures.
External links	Structure / PubMed:22727814 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	3.95 - 33.4 Å
Structure data	EMDB-5430: dATP-inhibited class Ia ribonucleotide reductase from E. coli: alpha4beta4 closed ring conformation Method: EM (single particle) / Resolution: 23.4 Å EMDB-5431: dATP-inhibited class Ia ribonucleotide reductase from E. coli: alpha4beta4 open conformation 1 Method: EM (single particle) / Resolution: 32.0 Å EMDB-5432: dATP-inhibited class Ia ribonucleotide reductase from E. coli: alpha4beta4 open conformation 2 Method: EM (single particle) / Resolution: 32.1 Å EMDB-5433: dATP-inhibited class Ia ribonucleotide reductase from E. coli: alpha4beta4 open conformation 3 Method: EM (single particle) / Resolution: 31.5 Å EMDB-5434: dATP-inhibited class Ia ribonucleotide reductase from E. coli: alpha4beta4 open conformation 4 Method: EM (single particle) / Resolution: 29.8 Å EMDB-5435: dATP-inhibited class Ia ribonucleotide reductase from E. coli: alpha4beta4 open conformation 5 Method: EM (single particle) / Resolution: 33.4 Å EMDB-5436: dATP-inhibited class Ia ribonucleotide reductase from E. coli: alpha4beta4 open conformation 6 Method: EM (single particle) / Resolution: 29.3 Å EMDB-5437: dATP-inhibited class Ia ribonucleotide reductase from E. coli: alpha4beta4 open conformation 7 Method: EM (single particle) / Resolution: 33.1 Å PDB-4erm: Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex at 4 Angstroms resolution Method: X-RAY DIFFRACTION / Resolution: 3.95 Å PDB-4erp: Crystal structure of a gemcitabine-diphosphate inhibited E. coli class Ia ribonucleotide reductase complex Method: X-RAY DIFFRACTION / Resolution: 4.45 Å
Chemicals	ChemComp-DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate ChemComp-DAT: 2'-DEOXYADENOSINE-5'-DIPHOSPHATE / Deoxyadenosine diphosphate ChemComp-MG: Unknown entry ChemComp-FEO: MU-OXO-DIIRON ChemComp-HOH: WATER / Water ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate
Source	Escherichia coli (E. coli) escherichia coli k-12 (bacteria)
Keywords	OXIDOREDUCTASE / protein-protein complex / alpha/beta barrel / atp cone / di-iron center / RNR alpha / RNR beta / thioredoxin / Ribonucleotide reduction / Cytosol / diiron center