5HS4

Plasmdoium Vivax Lactate dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.339 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition

Choi, S.J.Ban, C.

(2016) Sci Rep 6: 34998-34998

  • DOI: 10.1038/srep34998
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Structural elements are key elements for understanding single-stranded nucleic acid folding. Although various RNA structural elements have been documented, structural elements of single-stranded DNA (ssDNA) have rarely been reported. Herein, we deter ...

    Structural elements are key elements for understanding single-stranded nucleic acid folding. Although various RNA structural elements have been documented, structural elements of single-stranded DNA (ssDNA) have rarely been reported. Herein, we determined a crystal structure of PvLDH in complex with a DNA aptamer called pL1. This aptamer folds into a hairpin-bulge contact by adopting three novel structural elements, viz, DNA T-loop-like motif, base-phosphate zipper, and DNA G·G metal ion zipper. Moreover, the pL1:PvLDH complex shows unique properties compared with other protein:nucleic acid complexes. Generally, extensive intermolecular hydrogen bonds occur between unpaired nucleotides and proteins for specific recognitions. Although most protein-interacting nucleotides of pL1 are unpaired nucleotides, pL1 recognizes PvLDH by predominant shape complementarity with many bridging water molecules owing to the combination of three novel structural elements making protein-binding unpaired nucleotides stable. Moreover, the additional set of Plasmodium LDH residues which were shown to form extensive hydrogen bonds with unpaired nucleotides of 2008s does not participate in the recognition of pL1. Superimposition of the pL1:PvLDH complex with hLDH reveals steric clashes between pL1 and hLDH in contrast with no steric clashes between 2008s and hLDH. Therefore, specific protein recognition mode of pL1 is totally different from that of 2008s.


    Organizational Affiliation

    Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-lactate dehydrogenase
A
346Plasmodium vivaxMutation(s): 0 
Gene Names: LDH (ldh)
EC: 1.1.1.27
Find proteins for Q4PRK9 (Plasmodium vivax)
Go to UniProtKB:  Q4PRK9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.339 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.150 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 75.792α = 90.00
b = 80.613β = 90.00
c = 93.377γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-01-25 
  • Released Date: 2016-10-19 
  • Deposition Author(s): Choi, S.J., Ban, C.

Funding OrganizationLocationGrant Number
National Research Foundation of KoreaKorea, Republic OfNRF- 2015027587
National Research Foundation of KoreaKorea, Republic OfNRF-2014K1B1A1073720

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references