PDBsum entry 4z2b

Hydrolase/hydrolase inhibitor

PDB id: 4z2b

Contents

Protein chain

449 a.a.

Ligands

SO4

EDO ×2

TRS

4LC

Metals

_MG

Waters ×465

PDB id:

4z2b

Name:

Hydrolase/hydrolase inhibitor

Title:

The structure of human pde12 residues 161-609 in complex with gsk3036342a

Structure:

2',5'-phosphodiesterase 12. Chain: a. Fragment: unp residues 155-609. Synonym: 2-pde,mitochondrial deadenylase. Engineered: yes. Other_details: tev cloning tag on n-terminus

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pde12. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: de3

Resolution:

1.80Å R-factor: 0.183 R-free: 0.218

Authors:

R.T.Nolte,B.Wisely,L.Wang,E.R.Wood

Key ref:

E.R.Wood et al. (2015). The Role of Phosphodiesterase 12 (PDE12) as a Negative Regulator of the Innate Immune Response and the Discovery of Antiviral Inhibitors. J Biol Chem, 290, 19681-19696. PubMed id: 26055709 DOI: 10.1074/jbc.M115.653113

Date:

29-Mar-15 Release date: 17-Jun-15

Protein chain

Q6L8Q7  (PDE12_HUMAN) -  2',5'-phosphodiesterase 12 from Homo sapiens

Seq: 609 a.a.

Struc: 449 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.13.4 - poly(A)-specific ribonuclease.
• Reaction: Exonucleolytic cleavage of poly(A) to 5'-AMP.

DOI no: 10.1074/jbc.M115.653113

J Biol Chem 290:19681-19696 (2015)

PubMed id: 26055709

The Role of Phosphodiesterase 12 (PDE12) as a Negative Regulator of the Innate Immune Response and the Discovery of Antiviral Inhibitors.

E.R.Wood, R.Bledsoe, J.Chai, P.Daka, H.Deng, Y.Ding, S.Harris-Gurley, L.H.Kryn, E.Nartey, J.Nichols, R.T.Nolte, N.Prabhu, C.Rise, T.Sheahan, J.B.Shotwell, D.Smith, V.Tai, J.D.Taylor, G.Tomberlin, L.Wang, B.Wisely, S.You, B.Xia, H.Dickson.

ABSTRACT

2',5'-Oligoadenylate synthetase (OAS) enzymes and RNase-L constitute a major effector arm of interferon (IFN)-mediated antiviral defense. OAS produces a unique oligonucleotide second messenger, 2',5'-oligoadenylate (2-5A), that binds and activates RNase-L. This pathway is down-regulated by virus- and host-encoded enzymes that degrade 2-5A. Phosphodiesterase 12 (PDE12) was the first cellular 2-5A- degrading enzyme to be purified and described at a molecular level. Inhibition of PDE12 may up-regulate the OAS/RNase-L pathway in response to viral infection resulting in increased resistance to a variety of viral pathogens. We generated a PDE12-null cell line, HeLaΔPDE12, using transcription activator-like effector nuclease-mediated gene inactivation. This cell line has increased 2-5A levels in response to IFN and poly(I-C), a double-stranded RNA mimic compared with the parental cell line. Moreover, HeLaΔPDE12 cells were resistant to viral pathogens, including encephalomyocarditis virus, human rhinovirus, and respiratory syncytial virus. Based on these results, we used DNA-encoded chemical library screening to identify starting points for inhibitor lead optimization. Compounds derived from this effort raise 2-5A levels and exhibit antiviral activity comparable with the effects observed with PDE12 gene inactivation. The crystal structure of PDE12 complexed with an inhibitor was solved providing insights into the structure-activity relationships of inhibitor potency and selectivity.