4KFT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.241 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.181 

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, 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 preform ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Genome packaging NTPase B204
A, B, C, D
212Sulfolobus turreted icosahedral virus 2N/A
Find proteins for D5IEZ9 (Sulfolobus turreted icosahedral virus 2)
Go to UniProtKB:  D5IEZ9
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FLC
Query on FLC

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B, D
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
AGS
Query on AGS

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A, B, C, D
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.241 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.181 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 46.726α = 90.55
b = 65.185β = 93.65
c = 71.620γ = 91.59
Software Package:
Software NamePurpose
XDSdata reduction
SHARPphasing
XDSdata scaling
PHENIXrefinement
MxCuBEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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