1APA

X-RAY STRUCTURE OF A POKEWEED ANTIVIRAL PROTEIN, CODED BY A NEW GENOMIC CLONE, AT 0.23 NM RESOLUTION. A MODEL STRUCTURE PROVIDES A SUITABLE ELECTROSTATIC FIELD FOR SUBSTRATE BINDING.

Summary for 1APA

• Entry DOI: 10.2210/pdb1apa/pdb
• Descriptor: POKEWEED ANTIVIRAL PROTEIN (2 entities in total)
• Functional Keywords: antiviral protein, genomic clone
• Biological source: Phytolacca americana (American pokeweed)
• Cellular location: Secreted, cell wall: Q03464
• Total number of polymer chains: 1
• Total formula weight: 29766.08

Authors

Ago, H.,Kataoka, J.,Tsuge, H.,Habuka, N.,Inagaki, E.,Noma, M.,Miyano, M. (deposition date: 1993-09-21, release date: 1994-01-31, Last modification date: 2024-10-16)

Primary citation

Ago, H.,Kataoka, J.,Tsuge, H.,Habuka, N.,Inagaki, E.,Noma, M.,Miyano, M.
X-ray structure of a pokeweed antiviral protein, coded by a new genomic clone, at 0.23 nm resolution. A model structure provides a suitable electrostatic field for substrate binding.
Eur.J.Biochem., 225:369-374, 1994

PubMed Abstract: We have determined the crystal structure of alpha-pokeweed antiviral protein, a member of ribosome-inactivating proteins, at 0.23 nm resolution, by the molecular-replacement method. The crystals belong to the space group P2(1)2(1)2 with unit-cell dimensions a = 4.71, b = 11.63 and c = 4.96 nm, and contain one protein molecule/asymmetric unit based on a crystal volume/unit protein molecular mass of 2.1 x 10(-3) nm3/Da. The crystallographic residual value was reduced to 17.2% (0.6-0.23 nm resolution) with root-mean-square deviations in bond lengths of 1.9 pm and bond angles of 2.2 degrees. The C alpha-C alpha distance map shows that alpha-pokeweed antiviral protein is composed of three modules, the N-terminal (Ala1-Leu76), the central (Tyr77-Lys185) and the C-terminal (Tyr186-Thr266) modules. The substrate-binding site is formed as a cleft between the central and C-terminal modules and all the active residues exist on the central module. The electrostatic potential around the substrate-binding site shows that the central and C-terminal module sides of this cleft have a negatively and a positively charged region, respectively. This charge distribution in the protein seems to provide a suitable interaction with the substrate rRNA.

PubMed: 7925458
DOI: 10.1111/j.1432-1033.1994.00369.x

Experimental method

X-RAY DIFFRACTION (2.3 Å)