4KFU

Structure of the genome packaging NTPase B204 from Sulfolobus turreted icosahedral virus 2 in complex with AMPPCP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The Structure of the NTPase That Powers DNA Packaging into Sulfolobus Turreted Icosahedral Virus 2.

Happonen, L.J., Oksanen, E., Liljeroos, L., Goldman, A., Kajander, T., Butcher, S.J.

(2013) J Virol 87: 8388-8398

  • DOI: 10.1128/JVI.00831-13
  • Primary Citation of Related Structures:  
    4KFR, 4KFS, 4KFT, 4KFU

  • PubMed Abstract: 

    • Biochemical reactions powered by ATP hydrolysis are fundamental for the movement of molecules and cellular structures. One such reaction is the encapsidation of the double-stranded DNA (dsDNA) genome of an icosahedrally symmetric virus into a preformed procapsid with the help of a genome-translocating NTPase ...

    Biochemical reactions powered by ATP hydrolysis are fundamental for the movement of molecules and cellular structures. One such reaction is the encapsidation of the double-stranded DNA (dsDNA) genome of an icosahedrally symmetric virus into a preformed procapsid with the help of a genome-translocating NTPase. Such NTPases have been characterized in detail from both RNA and tailed DNA viruses. We present four crystal structures and the biochemical activity of a thermophilic NTPase, B204, from the nontailed, membrane-containing, hyperthermoacidophilic archaeal dsDNA virus Sulfolobus turreted icosahedral virus 2. These are the first structures of a genome-packaging NTPase from a nontailed, dsDNA virus with an archaeal host. The four structures highlight the catalytic cycle of B204, pinpointing the molecular movement between substrate-bound (open) and empty (closed) active sites. The protein is shown to bind both single-stranded and double-stranded nucleic acids and to have an optimum activity at 80°C and pH 4.5. The overall fold of B204 places it in the FtsK-HerA superfamily of P-loop ATPases, whose cellular and viral members have been suggested to share a DNA-translocating mechanism.

    Organizational Affiliation: 

    Institute of Biotechnology, University of Helsinki, Helsinki, Finland.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Genome packaging NTPase B204A, B, C, D212Sulfolobus turreted icosahedral virus 2Mutation(s): 0 
Gene Names: B204, STIV2_B204
EC: 3
Find proteins for D5IEZ9 (Sulfolobus turreted icosahedral virus 2)
Explore D5IEZ9 
Go to UniProtKB:  D5IEZ9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACP
Query on ACP
Download Ideal Coordinates CCD File 
 E [auth A], F [auth A], M [auth B], N [auth B], U [auth C], V [auth D]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N		 Ligand Interaction
FLC
Query on FLC
Download Ideal Coordinates CCD File 
 G [auth A], H [auth A], O [auth B], P [auth B]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
 L [auth A], T [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
 I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B], S [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.558α = 90.85
b = 65.227β = 93.77
c = 72.118γ = 91.56
Software Package:
Software NamePurpose
MxCuBEdata collection
SHARPphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-06-05
    Changes: Database references
  • Version 1.2: 2013-07-24
    Changes: Database references