PDBsum entry 3f23

Hydrolase

PDB id: 3f23

Contents

Protein chain

65 a.a. *

DNA/RNA

Waters ×60

* Residue conservation analysis

PDB id:

3f23

Name:

Hydrolase

Title:

Crystal structure of zalpha in complex with d(cggccg)

Structure:

Double-stranded RNA-specific adenosine deaminase. Chain: a, b, c. Fragment: n-terminal zalpha domain, unp residues 133-209. Synonym: drada, 136 kda double-stranded RNA-binding protein, p136, k88dsrbp, interferon-inducible protein 4, ifi-4. Engineered: yes. DNA (5'-d( Dtp Dcp Dgp Dgp Dcp Dcp Dg)-3'). Chain: d, e, f. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: adar1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Resolution:

2.70Å R-factor: 0.224 R-free: 0.264

Authors:

S.C.Ha,J.Choi,K.K.Kim

Key ref:

S.C.Ha et al. (2009). The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZ alpha(ADAR1). Nucleic Acids Res, 37, 629-637. PubMed id: 19074195

Date:

28-Oct-08 Release date: 30-Dec-08

Protein chains

P55265  (DSRAD_HUMAN) -  Double-stranded RNA-specific adenosine deaminase from Homo sapiens

Seq: 1226 a.a.

Struc: 65 a.a.

DNA/RNA chains

C-G-G-C-C-G 6 bases

C-G-G-C-C-G 6 bases

C-G-G-C-C-G 6 bases

Enzyme reactions

• Enzyme class: E.C.3.5.4.37 - double-stranded Rna adenine deaminase.
• Reaction: adenosine in double-stranded RNA + H2O + H⁺ = inosine in double- stranded RNA + NH4⁺

Nucleic Acids Res 37:629-637 (2009)

PubMed id: 19074195

The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZ alpha(ADAR1).

S.C.Ha, J.Choi, H.Y.Hwang, A.Rich, Y.G.Kim, K.K.Kim.

ABSTRACT

The Z-DNA conformation preferentially occurs at alternating purine-pyrimidine repeats, and is specifically recognized by Z alpha domains identified in several Z-DNA-binding proteins. The binding of Z alpha to foreign or chromosomal DNA in various sequence contexts is known to influence various biological functions, including the DNA-mediated innate immune response and transcriptional modulation of gene expression. For these reasons, understanding its binding mode and the conformational diversity of Z alpha bound Z-DNAs is of considerable importance. However, structural studies of Z alpha bound Z-DNA have been mostly limited to standard CG-repeat DNAs. Here, we have solved the crystal structures of three representative non-CG repeat DNAs, d(CACGTG)(2), d(CGTACG)(2) and d(CGGCCG)(2) complexed to hZ alpha(ADAR1) and compared those structures with that of hZ alpha(ADAR1)/d(CGCGCG)(2) and the Z alpha-free Z-DNAs. hZ alpha(ADAR1) bound to each of the three Z-DNAs showed a well conserved binding mode with very limited structural deviation irrespective of the DNA sequence, although varying numbers of residues were in contact with Z-DNA. Z-DNAs display less structural alterations in the Z alpha-bound state than in their free form, thereby suggesting that conformational diversities of Z-DNAs are restrained by the binding pocket of Z alpha. These data suggest that Z-DNAs are recognized by Z alpha through common conformational features regardless of the sequence and structural alterations.