4BLO

P4 PROTEIN FROM BACTERIOPHAGE PHI6 IN COMPLEX WITH ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Tracking in Atomic Detail the Functional Specializations in Viral Reca Helicases that Occur During Evolution.

El Omari, K.Meier, C.Kainov, D.Sutton, G.Grimes, J.M.Poranen, M.M.Bamford, D.H.Tuma, R.Stuart, D.I.Mancini, E.J.

(2013) Nucleic Acids Res. 41: 9396

  • DOI: 10.1093/nar/gkt713
  • Primary Citation of Related Structures:  
  • Also Cited By: 5MUW, 5MUV

  • 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, uses chemical energy to translocate single-stranded ...

    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.


    Organizational Affiliation

    Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK, Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00290 Helsinki, Finland, Department of Environmental Research, Siauliai University, Vilniaus gatvÄ— 88, 76285 Siauliai, Lithuania, Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK, Department of Biosciences, University of Helsinki, Biocenter 2, PO Box 56, 00014 Helsinki, Finland, Institute of Biotechnology, University of Helsinki, Biocenter 2, PO Box 56, 00014 Helsinki, Finland and Astbury Centre for Structural Molecular Biology and School of Cellular and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PACKAGING ENZYME P4
A, B, C, D, E, F, G, H, I, J, K, L
309Pseudomonas phage phi6Mutation(s): 0 
Gene Names: P4
EC: 3.6.1.15
Find proteins for P11125 (Pseudomonas phage phi6)
Go to UniProtKB:  P11125
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.217 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 93.840α = 82.46
b = 95.260β = 86.17
c = 98.330γ = 64.85
Software Package:
Software NamePurpose
HKL-2000data scaling
BUSTERrefinement
HKL-2000data reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-11-13
    Type: Database references