4PP4 | pdb_00004pp4

Minute virus of mice non-structural protein-1N-terminal nuclease domain reveals a unique Zn2+ coordination in the active site pocket and shows a novel mode of DNA recognition at the origin of replication

• PDB DOI: https://doi.org/10.2210/pdb4PP4/pdb

• Classification: REPLICATION
• Organism(s): Murine minute virus strain MVM prototype
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-02-26 Released: 2015-01-21 
• Deposition Author(s): Tewary, S.K., Zhao, H., Tang, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Structures of minute virus of mice replication initiator protein N-terminal domain: Insights into DNA nicking and origin binding.

Tewary, S.K., Liang, L., Lin, Z., Lynn, A., Cotmore, S.F., Tattersall, P., Zhao, H., Tang, L.

(2014) Virology 476C: 61-71

• PubMed: 25528417 
• DOI: https://doi.org/10.1016/j.virol.2014.11.022
• Primary Citation Related Structures: 
  3WRN, 3WRO, 3WRQ, 3WRR, 3WRS, 4PP4, 4R94


• PubMed Abstract: 
  

  Members of the Parvoviridae family all encode a non-structural protein 1 (NS1) that directs replication of single-stranded viral DNA, packages viral DNA into capsid, and serves as a potent transcriptional activator. Here we report the X-ray structure of the minute virus of mice (MVM) NS1 N-terminal domain at 1.45Å resolution, showing that sites for dsDNA binding, ssDNA binding and cleavage, nuclear localization, and other functions are integrated on a canonical fold of the histidine-hydrophobic-histidine superfamily of nucleases, including elements specific for this Protoparvovirus but distinct from its Bocaparvovirus or Dependoparvovirus orthologs. High resolution structural analysis reveals a nickase active site with an architecture that allows highly versatile metal ligand binding. The structures support a unified mechanism of replication origin recognition for homotelomeric and heterotelomeric parvoviruses, mediated by a basic-residue-rich hairpin and an adjacent helix in the initiator proteins and by tandem tetranucleotide motifs in the replication origins.

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Organizational Affiliation: 
• Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.
Departments of Laboratory Medicine, Yale University Medical School, New Haven, CT 06510, USA.
Departments of Laboratory Medicine, Yale University Medical School, New Haven, CT 06510, USA; Departments of Genetics, Yale University Medical School, New Haven, CT 06510, USA.
Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA. Electronic address: [e-mail].
Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.49 kDa 
• Atom Count: 2,323 
• Modeled Residue Count: 248 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-capsid protein NS-1	A	276	Murine minute virus strain MVM prototype	Mutation(s): 0  Gene Names: NS1 EC: 3.1.21 (UniProt), 3.6.4.12 (UniProt)
UniProt
Find proteins for P03134 (Murine minute virus (strain MVM prototype)) Explore P03134  Go to UniProtKB:  P03134

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BME	B [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
NA	C [auth A], D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.94	α = 90
b = 121.65	β = 90
c = 41.82	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-21 
Deposition Author(s): Tewary, S.K., Zhao, H., Tang, L.

Revision History  

• Version 1.0: 2015-01-21
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations