NAD+ ADP-ribosyltransferase

 

ADP-ribosyltransferase is a eukaryotic DNA binding protein that participates in cell recovery after DNA damage, particularly in base excision repair. After activation by binding to DNA strand-breaks it modifies itself (automodification) and other nuclear proteins (heteromodification) involved in chromatin architecture and DNA metabolism by covalent attachment of ADP-ribose units of NAD+ forming extended and branched polymers.

 

Reference Protein and Structure

Sequence
P26446 UniProt (2.4.2.-, 2.4.2.30) IPR008288 (Sequence Homologues) (PDB Homologues)
Biological species
Gallus gallus (Chicken) Uniprot
PDB
1a26 - THE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED WITH CARBA-NAD (2.25 Å) PDBe PDBsum 1a26
Catalytic CATH Domains
3.90.228.10 CATHdb (see all for 1a26)
Cofactors
Water (1)
Click To Show Structure

Enzyme Reaction (EC:2.4.2.30)

NAD(1-)
CHEBI:57540ChEBI
+
ADP-D-ribose(2-)
CHEBI:57967ChEBI
→
poly-ADP-D-ribose
CHEBI:61151ChEBI
+
nicotinamide
CHEBI:17154ChEBI
+
proton
CHEBI:24636ChEBI
Alternative enzyme names: ADP-ribosyltransferase (polymerizing), Poly(ADP-ribose) synthase, Poly(ADP-ribose)polymerase, Poly(ADP-ribose) synthetase, Poly(adenosine diphosphate ribose) polymerase, NAD(+):poly(adenine-diphosphate-D-ribosyl)-acceptor ADP-D-ribosyl-transferase, NAD(+):poly(adenosine-diphosphate-D-ribosyl)-acceptor ADP-D-ribosyl-transferase,

Enzyme Mechanism

Introduction

Glutamate deprotonates the 2' OH of the ADP-D-ribosyl-acceptor. The oxyanion then initiates a nucleophilic attack on the ribose carbon of ADP covalently attacked to the nicotinamide ring in a substitution reaction, eliminating nicotinamide with concomitant deprotonation of Glu988

Catalytic Residues Roles

UniProt PDB* (1a26)
Tyr904 Tyr907(254)A Has a non-polar interaction with the donor's pyridine ring and a hydrogen bond to the 3' OH of the acceptor - these are important for positioning the substrates to prevent attack in the wrong position. The 3' OH of the adenine-ribose is known to be required for full elongation. van der waals interaction, hydrogen bond donor, electrostatic stabiliser
Glu985 Glu988(335)A Deprotonates incoming acceptor and increases its nucleophilicity, and polarises the donor and acceptor by hydrogen bonding. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, electrostatic stabiliser
Ser901 Ser904(251)A Stabilises and binds the nicotinamide portion of the substrate. electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, overall reactant used, intermediate formation, bimolecular nucleophilic substitution, intermediate terminated, native state of enzyme regenerated, overall product formed

References

  1. Ruf A et al. (1998), J Mol Biol, 278, 57-65. The mechanism of the elongation and branching reaction of Poly(ADP-ribose) polymerase as derived from crystal structures and mutagenesis. DOI:10.1006/jmbi.1998.1673. PMID:9571033.
  2. Salmas RE et al. (2016), J Enzyme Inhib Med Chem, 31, 112-120. In silicoinvestigation of PARP-1 catalytic domains inholoandapostates for the design of high-affinity PARP-1 inhibitors. DOI:10.3109/14756366.2015.1005011. PMID:26083304.
  3. Halder AK et al. (2015), J Biomol Struct Dyn, 33, 1756-1779. Stepwise development of structure–activity relationship of diverse PARP-1 inhibitors through comparative and validatedin silico modeling techniques and molecular dynamics simulation. DOI:10.1080/07391102.2014.969772. PMID:25350685.
  4. Langelier MF et al. (2013), Curr Opin Struct Biol, 23, 134-143. PARP-1 mechanism for coupling DNA damage detection to poly(ADP-ribose) synthesis. DOI:10.1016/j.sbi.2013.01.003. PMID:23333033.
  5. Wang Y et al. (2011), J Biomol Struct Dyn, 28, 881-893. The Key Residues of Active Sites on the Catalytic Fragment for Paclitaxel Interacting with Poly (ADP-Ribose) Polymerase. DOI:10.1080/07391102.2011.10508615. PMID:21469749.

Step 1. Glu988 deprotonates the 2'-OH of the ADP-D-ribosyl-acceptor.

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Catalytic Residues Roles

Residue Roles
Tyr907(254)A hydrogen bond donor, van der waals interaction
Glu988(335)A hydrogen bond acceptor
Ser904(251)A electrostatic stabiliser
Glu988(335)A proton acceptor

Chemical Components

proton transfer, overall reactant used, intermediate formation

Step 2. The oxyanion initiates a nucleophilic attack on the ribose carbon of ADP covalently attacked to the nicotinamide ring in a substitution reaction, eliminating nicotinamide with concomitant deprotonation of Glu988.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Tyr907(254)A hydrogen bond donor, van der waals interaction, electrostatic stabiliser
Glu988(335)A hydrogen bond donor, hydrogen bond acceptor, electrostatic stabiliser
Ser904(251)A electrostatic stabiliser
Glu988(335)A proton donor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic substitution, overall reactant used, intermediate terminated, native state of enzyme regenerated, overall product formed

Step 3. In an inferred step, the nicotinamide loses a proton to the solvent, and the final product is generated.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles

Chemical Components

overall product formed, proton transfer
Download: Image, Marvin File

Step 1. Glu988 deprotonates the 2'-OH of the ADP-D-ribosyl-acceptor.

Step 2. The oxyanion initiates a nucleophilic attack on the ribose carbon of ADP covalently attacked to the nicotinamide ring in a substitution reaction, eliminating nicotinamide with concomitant deprotonation of Glu988.

Step 3. In an inferred step, the nicotinamide loses a proton to the solvent, and the final product is generated.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, Gail J. Bartlett, James W. Murray, Craig Porter