PDBsum entry: 1lpd

Antiviral protein

PDB id: 1lpd

Contents

Protein chain

254 a.a. *

Ligands

ADE

Waters ×190

* Residue conservation analysis

PDB id:

1lpd

Name:

Antiviral protein

Title:

High resolution structure of recombinant dianthin antiviral protein-potent anti-HIV agent (complex with adenine)

Structure:

Dianthin 30. Chain: a. Synonym: antiviral protein dap-30, rrna n-glycosylase, rrna n-glycosidase, ribosome-inactivating protein. Engineered: yes

Source:

Dianthus caryophyllus. Clove pink. Organism_taxid: 3570. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.70Å R-factor: 0.170 R-free: 0.230

Authors:

I.V.Kurinov,F.Rajamohan,F.M.Uckun

Key ref:

I.V.Kurinov et al. (2004). High resolution X-ray structure and potent anti-HIV activity of recombinant dianthin antiviral protein. Arzneimittelforschung, 54, 692-702. PubMed id: 15553110

Date:

07-May-02 Release date: 11-May-04

Protein chain

P24476  (RIP0_DIACA) -  Antiviral protein DAP-30

Seq: 293 a.a.

Struc: 254 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.2.2.22 - rRNA N-glycosylase.
• Reaction: Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.

 Gene Ontology (GO) functional annotation 

• Biological process: defense response (4 terms)
• Biochemical function: hydrolase activity (2 terms)

Arzneimittelforschung 54:692-702 (2004)

PubMed id: 15553110

High resolution X-ray structure and potent anti-HIV activity of recombinant dianthin antiviral protein.

I.V.Kurinov, F.Rajamohan, F.M.Uckun.

ABSTRACT

Dianthin antiviral protein (DAP) is a naturally occurring antiviral protein from the leaves of carnation (Dianthus caryophyllus) capable of depurinating HIV-1 RNA and inhibiting HIV-1 replication in human peripheral blood mononuclear cells. Escherichia coli-derived recombinant DAP (rDAP, amino acids 1-254) was purified to homogeneity for structural and functional studies. In the following paper the X-ray crystal structure of rDAP as well as its complexes with cyclic AMP and adenyl-guanosine (ApG) as substrate analogs at 1.7 A resolution are reported. Molecular modeling studies of the interactions of DAP and the structurally similar pokeweed antiviral protein (PAP) with a single-stranded RNA heptamer predicted a more potent anti-HIV activity for rDAP due to its unique surface topology and more favorable charge distribution in its 20 A-long RNA binding active center cleft. In accordance with the predictions of the modeling studies, rDAP was more potent than rPAP in depurinating HIV-1 RNA. To the knowledge of the authors, this is the first structural and functional characterization of recombinant DAP.