PDBsum entry 2nyt

Hydrolase

PDB id: 2nyt

Contents

Protein chain

185 a.a. *

Metals

_ZN ×4

Waters ×88

* Residue conservation analysis

PDB id:

2nyt

Name:

Hydrolase

Title:

The apobec2 crystal structure and functional implications for aid

Structure:

ProbablE C->u-editing enzyme apobec-2. Chain: a, b, c, d. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: apobec2. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.246 R-free: 0.295

Authors:

C.Prochnow,R.Bransteitter,M.Klein,M.Goodman,X.Chen

Key ref:

C.Prochnow et al. (2007). The APOBEC-2 crystal structure and functional implications for the deaminase AID. Nature, 445, 447-451. PubMed id: 17187054 DOI: 10.1038/nature05492

Date:

21-Nov-06 Release date: 09-Jan-07

Protein chains

Q9Y235  (ABEC2_HUMAN) -  C->U-editing enzyme APOBEC-2 from Homo sapiens

Seq: 224 a.a.

Struc: 185 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.5.4.36 - mRNA(cytosine(6666)) deaminase.
• Reaction: cytidine₆₆₆₆ in apoB mRNA + H2O + H⁺ = uridine₆₆₆₆ in apoB mRNA + NH4⁺

DOI no: 10.1038/nature05492

Nature 445:447-451 (2007)

PubMed id: 17187054

The APOBEC-2 crystal structure and functional implications for the deaminase AID.

C.Prochnow, R.Bransteitter, M.G.Klein, M.F.Goodman, X.S.Chen.

ABSTRACT

APOBEC-2 (APO2) belongs to the family of apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) polypeptides, which deaminates mRNA and single-stranded DNA. Different APOBEC members use the same deamination activity to achieve diverse human biological functions. Deamination by an APOBEC protein called activation-induced cytidine deaminase (AID) is critical for generating high-affinity antibodies, and deamination by APOBEC-3 proteins can inhibit retrotransposons and the replication of retroviruses such as human immunodeficiency virus and hepatitis B virus. Here we report the crystal structure of APO2. APO2 forms a rod-shaped tetramer that differs markedly from the square-shaped tetramer of the free nucleotide cytidine deaminase, with which APOBEC proteins share considerable sequence homology. In APO2, two long alpha-helices of a monomer structure prevent the formation of a square-shaped tetramer and facilitate formation of the rod-shaped tetramer via head-to-head interactions of two APO2 dimers. Extensive sequence homology among APOBEC family members allows us to test APO2 structure-based predictions using AID. We show that AID deamination activity is impaired by mutations predicted to interfere with oligomerization and substrate access. The structure suggests how mutations in patients with hyper-IgM-2 syndrome inactivate AID, resulting in defective antibody maturation.

Selected figure(s)

Figure 2.
Figure 2: The APO2 active site. a, The APO2 active sites are accessible to DNA/RNA. Red spheres represent Zn. b, The fntCDA active site is accessible only to free nucleotides. c, The outer APO2 active sites show Zn coordination (yellow dashed lines) by three residues (H98, C128, C131) and a water molecule (blue sphere). d, The middle APO2 active centre sites show Zn coordination by a fourth residue, E60. e, In the 1'-hairpin structure, the hydrophobic ring of Y61 interacts with the guanidine group of R65, stabilizing the conformation. f, In the h1/ 1 loop, the E60 coordinates with Zn. Y61 now rotates away from R65 and interacts with R57, facilitating the disruption of the 1'-hairpin and stabilizing the loop conformation. g, Superimposed monomers show that the h1/ 1 loop (purple) is pulled down 8.5 Å towards the active site owing to the E60–Zn bond formation.

Figure 4.
Figure 4: AID HIGM-2 mutations.
Figure 4 : AID HIGM-2 mutations. Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg@nature.com-
a, Alignment of mutated residues of AID from HIGM-2 patients with the corresponding residues in APO2, showing high sequence conservation. b, Mapping the residues in AID HIGM-2 mutations (R112, L113, N168) to the tetramer interface as modelled from the APO2 structure. c, Mapping the AID HIGM-2 mutations, S83 and S85, near the active site. d, Mapping the AID mutations, K16, Y114/F115 and C116 (in green), to the exposed surface of an outer monomer. The HIGM-2 AID residues (R112, L113, N168, in yellow), which are at the tetramer interface (b), are also located on this exposed surface. e, Mapping of AID HIGM-2 mutations, W80, L106, M139 and F151, to the interior core structure.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 445, 447-451) copyright 2007.

Figures were selected by an automated process.