PDBsum entry: 1zy7

Hydrolase

PDB id: 1zy7

Contents

Protein chains

378 a.a. *

Ligands

IHP ×2

SO4

Metals

_ZN ×2

Waters ×669

* Residue conservation analysis

PDB id:

1zy7

Name:

Hydrolase

Title:

Crystal structure of the catalytic domain of an adenosine deaminase that acts on RNA (hadar2) bound to inositol hexakisphosphate (ihp)

Structure:

RNA-specific adenosine deaminase b1, isoform drada2a. Chain: a, b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.

Biol. unit:

Monomer (from PQS)

Resolution:

1.70Å R-factor: 0.175 R-free: 0.206

Authors:

M.R.Macbeth,H.L.Schubert,A.P.Vandemark,A.T.Lingam,C.P.Hill, B.L.Bass

Key ref:

M.R.Macbeth et al. (2005). Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing. Science, 309, 1534-1539. PubMed id: 16141067 DOI: 10.1126/science.1113150

Date:

09-Jun-05 Release date: 13-Sep-05

Protein chains

P78563  (RED1_HUMAN) -  Double-stranded RNA-specific editase 1

Seq: 741 a.a.

Struc: 378 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: RNA processing (1 term)
• Biochemical function: RNA binding (2 terms)

DOI no: 10.1126/science.1113150

Science 309:1534-1539 (2005)

PubMed id: 16141067

Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing.

M.R.Macbeth, H.L.Schubert, A.P.Vandemark, A.T.Lingam, C.P.Hill, B.L.Bass.

ABSTRACT

We report the crystal structure of the catalytic domain of human ADAR2, an RNA editing enzyme, at 1.7 angstrom resolution. The structure reveals a zinc ion in the active site and suggests how the substrate adenosine is recognized. Unexpectedly, inositol hexakisphosphate (IP6) is buried within the enzyme core, contributing to the protein fold. Although there are no reports that adenosine deaminases that act on RNA (ADARs) require a cofactor, we show that IP6 is required for activity. Amino acids that coordinate IP6 in the crystal structure are conserved in some adenosine deaminases that act on transfer RNA (tRNA) (ADATs), related enzymes that edit tRNA. Indeed, IP6 is also essential for in vivo and in vitro deamination of adenosine 37 of tRNAala by ADAT1.

Selected figure(s)

Figure 1.
Fig. 1. (A) ADAR catalyzed hydrolytic deamination of adenosine to inosine in dsRNA. (B) Ribbon model of hADAR2-D. The active-site zinc atom is represented by a magenta sphere. The N-terminal /ß domain (residues 306 to 620) is colored cyan, with the region that shares structural similarity with CDA and TadA colored dark blue (deamination motif; residues 350 to 375, 392 to 416, 439 to 455, 514 to 525, and 542 to 551). The C-terminal helical domain (residues 621 to 700), which with contributions from the deamination motif makes the major contacts to IP[6] (ball and stick), is colored red. Ends of the disordered segment (residues 462 to 473) are indicated with asterisks. (C) Residue interactions at the active site. Shown are the zinc ion, coordinating residues (H394, C451, and C516), the nucleophilic water (blue sphere), and the proposed proton-shuttling residue, E396. The hydrogen-bond relay that connects the active site to the IP[6] is also indicated. Single-letter abbreviations for amino acid residues are defined in (42).

Figure 5.
Fig. 5. (A) Schematic diagram showing the relative lengths and domain structures of hADAR2 and family members from S. cerevisiae (sc) and E. coli (ec). Proteins are anchored at the invariant zinc-coordinating histidine (H). Residues that coordinate IP[6] are red lines; double-stranded RNA binding motifs are in black. Alignments for regions surrounding the residues that coordinate IP[6] in hADAR2 are shown below, with blue numbering corresponding to hADAR2. IP[6] coordinating residues are in red, with side-chain contacts in bold. Residues N391, W523, Q669, W687, E689, and D695 are water-mediated contacts. The conserved K483, which is part of a hydrogen-bond relay from IP[6] to the active site zinc, is shown in green. Sequences diverge considerably in the region surrounding K483; the alignment shown was chosen because the conserved lysine of various subfamilies is aligned with K483 of hADAR2. Notably, the IP[6] coordinating residues are found in ADAR3, which suggests that inefficient IP[6] binding is not the reason this enzyme lacks deaminase activity (43). (B) The tRNA^ala substrate used in this study showing the sites of modification by the ADAT proteins. Single-letter abbreviations for amino acid residues are defined in (42).

The above figures are reprinted by permission from the AAAs: Science (2005, 309, 1534-1539) copyright 2005.

Figures were selected by an automated process.