1LLN image
Deposition Date 2002-04-29
Release Date 2003-06-17
Last Version Date 2025-03-26
Entry Detail
PDB ID:
1LLN
Keywords:
Title:
1.6A CRYSTAL STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN-III (PAP-III) WITH METHYLATED LYSINES
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.60 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 31 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Antiviral Protein 3
Gene (Uniprot):PAP2
Chain IDs:A
Chain Length:262
Number of Molecules:1
Biological Source:Phytolacca americana
Primary Citation
High resolution X-ray structure of potent anti-HIV pokeweed antiviral protein-III
Biochem.Pharm. 65 1709 1717 (2003)
PMID: 12754107 DOI: 10.1016/S0006-2952(03)00144-8

Abstact

Pokeweed antiviral protein III (PAP-III), a naturally occurring protein isolated from late summer leaves of the pokeweed plant (Phytolacca americana), has potent anti-HIV activity by an as yet undetermined molecular mechanism. PAP-III belongs to a family of ribosome-inactivating proteins that catalytically deadenylate ribosomal and viral RNA. The chemical modification of PAP-III by reductive methylation of its lysine residues significantly improved the crystal quality for X-ray diffraction studies. Trigonal crystals of the modified PAP-III, with unit cell parameters a=b=80.47A, c=76.21A, were obtained using 30% PEG400 as the precipitant. These crystals contained one enzyme molecule per asymmetric unit and diffracted up to 1.5A, when exposed to a synchrotron source. Here we report the X-ray crystal structure of PAP-III at 1.6A resolution, which was solved by molecular replacement using the homology model of PAP-III as a search model. The fold typical of other ribosome-inactivating proteins is conserved, despite several differences on the surface and in the loop regions. Residues Tyr(69), Tyr(117), Glu(172), and Arg(175) are expected to define the active site of PAP-III. Molecular modeling studies of the interactions of PAP-III and PAP-I with a single-stranded RNA heptamer predicted a more potent anti-HIV activity for PAP-III due to its unique surface topology and more favorable charge distribution in its 20A-long RNA binding active center cleft. In accordance with the predictions of the modeling studies, PAP-III was more potent than PAP-I in depurinating HIV-1 RNA.

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