PDBsum entry 2fp0

Hydrolase

PDB id: 2fp0

Contents

Protein chain

339 a.a. *

Metals

_MG ×4

Waters ×147

* Residue conservation analysis

PDB id:

2fp0

Name:

Hydrolase

Title:

Human adp-ribosylhydrolase 3

Structure:

Adp-ribosylhydrolase like 2. Chain: a, b. Fragment: residues 19-347. Engineered: yes

Source:

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

Resolution:

2.05Å R-factor: 0.189 R-free: 0.231

Authors:

C.Mueller-Dieckmann,M.S.Weiss,F.Koch-Nolte

Key ref:

C.Mueller-Dieckmann et al. (2006). The structure of human ADP-ribosylhydrolase 3 (ARH3) provides insights into the reversibility of protein ADP-ribosylation. Proc Natl Acad Sci U S A, 103, 15026-15031. PubMed id: 17015823 DOI: 10.1073/pnas.0606762103

Date:

15-Jan-06 Release date: 10-Oct-06

Protein chains

Q9NX46  (ARHL2_HUMAN) -  ADP-ribosylhydrolase ARH3 from Homo sapiens

Seq: 363 a.a.

Struc: 339 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.2.1.143 - poly(ADP-ribose) glycohydrolase.
• Pathway: Poly(ADP-ribose) Glycohydrolase
• Reaction: [(1''->2')-ADP-alpha-D-ribose](n) + H2O = [(1''->2')-ADP-alpha-D- ribose](n-1) + ADP-D-ribose

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1073/pnas.0606762103

Proc Natl Acad Sci U S A 103:15026-15031 (2006)

PubMed id: 17015823

The structure of human ADP-ribosylhydrolase 3 (ARH3) provides insights into the reversibility of protein ADP-ribosylation.

C.Mueller-Dieckmann, S.Kernstock, M.Lisurek, J.P.von Kries, F.Haag, M.S.Weiss, F.Koch-Nolte.

ABSTRACT

Posttranslational modifications are used by cells from all kingdoms of life to control enzymatic activity and to regulate protein function. For many cellular processes, including DNA repair, spindle function, and apoptosis, reversible mono- and polyADP-ribosylation constitutes a very important regulatory mechanism. Moreover, many pathogenic bacteria secrete toxins which ADP-ribosylate human proteins, causing diseases such as whooping cough, cholera, and diphtheria. Whereas the 3D structures of numerous ADP-ribosylating toxins and related mammalian enzymes have been elucidated, virtually nothing is known about the structure of protein de-ADP-ribosylating enzymes. Here, we report the 3Dstructure of human ADP-ribosylhydrolase 3 (hARH3). The molecular architecture of hARH3 constitutes the archetype of an all-alpha-helical protein fold and provides insights into the reversibility of protein ADP-ribosylation. Two magnesium ions flanked by highly conserved amino acids pinpoint the active-site crevice. Recombinant hARH3 binds free ADP-ribose with micromolar affinity and efficiently de-ADP-ribosylates poly- but not monoADP-ribosylated proteins. Docking experiments indicate a possible binding mode for ADP-ribose polymers and suggest a reaction mechanism. Our results underscore the importance of endogenous ADP-ribosylation cycles and provide a basis for structure-based design of ADP-ribosylhydrolase inhibitors.

Selected figure(s)

Figure 1.
Fig. 1. Posttranslational modification of proteins by reversible ADP-ribosylation. ARTs and PARPs transfer the ADP-ribose (ADPR) moiety from -NAD onto specific amino acid side chains or onto ADPR moieties (X) of target proteins under the release of nicotinamide. This modification may lead to either activation or inactivation of the target protein. Protein-ADP-ribosylhydrolases (ARHs and PARGs) hydrolyze the -glycosidic bond between ADPR and the side chain, thereby restoring normal protein function. X can be Arg, Asp, Cys, diphthamide, Glu, or ADPR. In the case of mono-ADP-ribosylation, R and R' are OH groups. In the case of polyADP-ribosylation, attachment of ADPR can take place at the R site (elongation) or at the R' site (branching). In mammals, two distinct subfamilies of ARTs (ART1–5, PARP1–17) and two distinct subfamilies of ARHs (ARH1–3, PARG) exist.

Figure 3.
Fig. 3. Active site of ARH3. (A) Coordination of Mg^2+ ions in the orthorhombic crystal form of hARH3. Hydrogen bonds are represented as dashed lines. (B) Superposition of the Mg^2+-coordinating residues of the orthorhombic (gray) and monoclinic crystal forms. Residue Asp-300 is slightly shifted but retains its bidentate binding character, whereas Glu-25 of the monoclinic crystal form is shifted by 1.8 Å with respect to those of the orthorhombic crystal form. The residues from the monoclinic crystal form are shown in color.

Figures were selected by an automated process.