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	Tracking in atomic detail the functional specializations in viral RecA helicases that occur during evolution.
Journal, issue, pages	Nucleic Acids Res, Vol. 41, Issue 20, Page 9396-9410, Year 2013
Publish date	Aug 11, 2013
Authors	Kamel El Omari / Christoph Meier / Denis Kainov / Geoff Sutton / Jonathan M Grimes / Minna M Poranen / Dennis H Bamford / Roman Tuma / David I Stuart / Erika J Mancini /
PubMed Abstract	Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, ...Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, uses chemical energy to translocate single-stranded RNA genomic precursors into the procapsid. We previously dissected the mechanism of RNA translocation for one such phage, 12, and have now investigated three further highly divergent, cystoviral P4 NTPases (from 6, 8 and 13). High-resolution crystal structures of the set of P4s allow a structure-based phylogenetic analysis, which reveals that these proteins form a distinct subfamily of the RecA-type ATPases. Although the proteins share a common catalytic core, they have different specificities and control mechanisms, which we map onto divergent N- and C-terminal domains. Thus, the RNA loading and tight coupling of NTPase activity with RNA translocation in 8 P4 is due to a remarkable C-terminal structure, which wraps right around the outside of the molecule to insert into the central hole where RNA binds to coupled L1 and L2 loops, whereas in 12 P4, a C-terminal residue, serine 282, forms a specific hydrogen bond to the N7 of purines ring to confer purine specificity for the 12 enzyme.
External links	Nucleic Acids Res / PubMed:23939620 / PubMed Central
Methods	X-ray diffraction
Resolution	1.7 - 3.1 Å
Structure data	PDB-4blo: P4 PROTEIN FROM BACTERIOPHAGE PHI6 IN COMPLEX WITH ADP Method: X-RAY DIFFRACTION / Resolution: 2.8 Å PDB-4blp: P4 PROTEIN FROM BACTERIOPHAGE PHI13 Method: X-RAY DIFFRACTION / Resolution: 1.7 Å PDB-4blq: P4 PROTEIN FROM BACTERIOPHAGE PHI8 Method: X-RAY DIFFRACTION / Resolution: 2.79 Å PDB-4blr: P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH UTP Method: X-RAY DIFFRACTION / Resolution: 1.9 Å PDB-4bls: P4 PROTEIN FROM BACTERIOPHAGE PHI12 Q278A MUTANT IN COMPLEX WITH AMPcPP Method: X-RAY DIFFRACTION / Resolution: 2.6 Å PDB-4blt: P4 PROTEIN FROM BACTERIOPHAGE PHI12 S292A MUTANT IN COMPLEX WITH AMPcPP Method: X-RAY DIFFRACTION / Resolution: 2.4 Å PDB-4bwy: P4 PROTEIN FROM BACTERIOPHAGE PHI8 (R32) Method: X-RAY DIFFRACTION / Resolution: 3.1 Å
Chemicals	ChemComp-CA: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-FLC: CITRATE ANION ChemComp-GOL: GLYCEROL ChemComp-HOH: WATER ChemComp-UTP: URIDINE 5'-TRIPHOSPHATE / UTPYM ChemComp-DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE ChemComp-APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / AMP-CPP, energy-carrying molecule analogue*YM
Source	pseudomonas phage phi6 (bacteriophage) pseudomonas phage phi13 (bacteriophage) pseudomonas phage phi8 (bacteriophage) pseudomonas phage phi12 (bacteriophage)
Keywords	HYDROLASE / ATPASE / CYSTOVIRIDAE / NTPASE / PACKAGING