2RVC | pdb_00002rvc

Solution structure of Zalpha domain of goldfish ZBP-containing protein kinase

• PDB DOI: https://doi.org/10.2210/pdb2RVC/pdb
• BMRB: 11595

• Classification: DNA BINDING PROTEIN
• Organism(s): Carassius auratus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-08 Released: 2016-02-03 
• Deposition Author(s): Lee, A., Park, C., Park, J., Kwon, M., Choi, Y., Kim, K., Choi, B., Lee, J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of the Z-DNA binding domain of PKR-like protein kinase from Carassius auratus and quantitative analyses of the intermediate complex during B-Z transition.

Lee, A.R., Park, C.J., Cheong, H.K., Ryu, K.S., Park, J.W., Kwon, M.Y., Lee, J., Kim, K.K., Choi, B.S., Lee, J.H.

(2016) Nucleic Acids Res 44: 2936-2948

• PubMed: 26792893 
• DOI: https://doi.org/10.1093/nar/gkw025
• Primary Citation Related Structures: 
  2RVC


• PubMed Abstract: 
  

  Z-DNA binding proteins (ZBPs) play important roles in RNA editing, innate immune response and viral infection. Structural and biophysical studies show that ZBPs initially form an intermediate complex with B-DNA for B-Z conversion. However, a comprehensive understanding of the mechanism of Z-DNA binding and B-Z transition is still lacking, due to the absence of structural information on the intermediate complex. Here, we report the solution structure of the Zα domain of the ZBP-containing protein kinase from Carassius auratus(caZαPKZ). We quantitatively determined the binding affinity of caZαPKZ for both B-DNA and Z-DNA and characterized its B-Z transition activity, which is modulated by varying the salt concentration. Our results suggest that the intermediate complex formed by caZαPKZ and B-DNA can be used as molecular ruler, to measure the degree to which DNA transitions to the Z isoform.

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Organizational Affiliation: 
• Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Republic of Korea.
Division of Liberal Arts and Sciences and Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.
Division of Magnetic Resonance, KBSI, Chungbuk 28119, Republic of Korea.
Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Republic of Korea Division of Magnetic Resonance, KBSI, Chungbuk 28119, Republic of Korea.
Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.
Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Gyeonggi 16419, Republic of Korea.
Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Republic of Korea [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.46 kDa 
• Atom Count: 520 
• Modeled Residue Count: 64 
• Deposited Residue Count: 64 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon-inducible and double-stranded-dependent eIF-2kinase	A	64	Carassius auratus	Mutation(s): 0
UniProt
Find proteins for Q7T2M9 (Carassius auratus) Explore Q7T2M9  Go to UniProtKB:  Q7T2M9

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Lee, A., Park, C., Park, J., Kwon, M., Choi, Y., Kim, K., Choi, B., Lee, J.

Revision History  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references