1QGP | pdb_00001qgp

NMR STRUCTURE OF THE Z-ALPHA DOMAIN OF ADAR1, 15 STRUCTURES

• PDB DOI: https://doi.org/10.2210/pdb1QGP/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-05-03 Released: 1999-10-19 
• Deposition Author(s): Schade, M., Turner, C.J., Kuehne, R., Schmieder, P., Lowenhaupt, K., Herbert, A., Rich, A., Oschkinat, H.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 15 
• Selection Criteria: LEAST RESTRAINT VIOLATION AND LOWEST ENERGY 

Literature

The solution structure of the Zalpha domain of the human RNA editing enzyme ADAR1 reveals a prepositioned binding surface for Z-DNA.

Schade, M., Turner, C.J., Kuhne, R., Schmieder, P., Lowenhaupt, K., Herbert, A., Rich, A., Oschkinat, H.

(1999) Proc Natl Acad Sci U S A 96: 12465-12470

• PubMed: 10535945 
• DOI: https://doi.org/10.1073/pnas.96.22.12465
• Primary Citation Related Structures: 
  1QGP


• PubMed Abstract: 
  

  Double-stranded RNA deaminase I (ADAR1) contains the Z-DNA binding domain Zalpha. Here we report the solution structure of free Zalpha and map the interaction surface with Z-DNA, confirming roles previously assigned to residues by mutagenesis. Comparison with the crystal structure of the (Zalpha)(2)/Z-DNA complex shows that most Z-DNA contacting residues in free Zalpha are prepositioned to bind Z-DNA, thus minimizing the entropic cost of binding. Comparison with homologous (alpha+beta)helix-turn-helix/B-DNA complexes suggests that binding of Zalpha to B-DNA is disfavored by steric hindrance, but does not eliminate the possibility that related domains may bind to both B- and Z-DNA.

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Organizational Affiliation: 
• Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.61 kDa 
• Atom Count: 601 
• Modeled Residue Count: 76 
• Deposited Residue Count: 77 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (DOUBLE STRANDED RNA ADENOSINE DEAMINASE)	A	77	Homo sapiens	Mutation(s): 1  EC: 3.5.4.37
UniProt & NIH Common Fund Data Resources
Find proteins for P55265 (Homo sapiens) Explore P55265  Go to UniProtKB:  P55265
PHAROS:  P55265 GTEx:  ENSG00000160710

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 15 
• Selection Criteria: LEAST RESTRAINT VIOLATION AND LOWEST ENERGY 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-10-19 
Deposition Author(s): Schade, M., Turner, C.J., Kuehne, R., Schmieder, P., Lowenhaupt, K., Herbert, A., Rich, A., Oschkinat, H.

Revision History  

• Version 1.0: 1999-10-19
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2023-12-27
  Changes: Data collection