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 

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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)  |  3D 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
UniProt
Find proteins for D5IEZ9 (Sulfolobus turreted icosahedral virus 2)
Explore D5IEZ9 
Go to UniProtKB:  D5IEZ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5IEZ9
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],
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],
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