PDBsum entry: 1ncp

Viral protein

PDB id: 1ncp

Contents

Protein chains

17 a.a.

18 a.a.

Metals

_ZN ×2

PDB id:

1ncp

Name:

Viral protein

Title:

Structural characterization of a 39 residue synthetic peptide containing the two zinc binding domains from the HIV-1 p7 nucleocapsid protein by cd and nmr spectroscopy

Structure:

HIV-1 p7 nucleocapsid protein. Chain: n. Engineered: yes. HIV-1 p7 nucleocapsid protein. Chain: c. Engineered: yes

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Organism_taxid: 11676

NMR struc:

1 models

Authors:

G.M.Clore,J.G.Omichinski,A.M.Gronenborn

Key ref:

J.G.Omichinski et al. (1991). Structural characterization of a 39-residue synthetic peptide containing the two zinc binding domains from the HIV-1 p7 nucleocapsid protein by CD and NMR spectroscopy. FEBS Lett, 292, 25-30. PubMed id: 1959614 DOI: 10.1016/0014-5793(91)80825-N

Date:

27-Nov-91 Release date: 31-Oct-93

Protein chain

P04585  (POL_HV1H2) -  Gag-Pol polyprotein

Seq: 1435 a.a.

Struc: 17 a.a.

Protein chain

P24740  (POL_HV1U4) -  Gag-Pol polyprotein

Seq: 1428 a.a.

Struc: 18 a.a.

Enzyme reactions

• Enzyme class 1: Chains N, C: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
• Enzyme class 2: Chains N, C: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
• Enzyme class 3: Chains N, C: E.C.3.1.13.2 - Exoribonuclease H.
• Reaction: Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
• Enzyme class 4: Chains N, C: E.C.3.1.26.13 - Retroviral ribonuclease H.
• Enzyme class 5: Chains N, C: E.C.3.4.23.16 - HIV-1 retropepsin.
• Reaction: Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (2 terms)

reference

DOI no: 10.1016/0014-5793(91)80825-N

FEBS Lett 292:25-30 (1991)

PubMed id: 1959614

Structural characterization of a 39-residue synthetic peptide containing the two zinc binding domains from the HIV-1 p7 nucleocapsid protein by CD and NMR spectroscopy.

J.G.Omichinski, G.M.Clore, K.Sakaguchi, E.Appella, A.M.Gronenborn.

ABSTRACT

A 39-residue peptide (p7-DF) containing the two zinc binding domains of the p7 nucleocapsid protein was prepared by solid-phase peptide synthesis. The solution structure of the peptide was characterized using circular dichroic and nuclear magnetic resonance spectroscopy in both the presence and absence of zinc ions. Circular dichroic spectroscopy indicates that the peptide exhibits a random coil conformation in the absence of zinc but appears to form an ordered structure in the presence of zinc. Two-dimensional nuclear magnetic resonance spectroscopy indicates that the two zinc binding domains within the peptide form stable, but independent, units upon the addition of 2 equivalents of ZnCl2 per equivalent of peptide. Structure calculations on the basis of nuclear Overhauser (NOE) data indicate that the two zinc binding domains have the same polypeptide fold within the errors of the coordinates (approximately 0.5 A for the backbone atoms, the zinc atoms and the coordinating cysteine and histidine ligands). The linker region (Arg17-Gly23) is characterized by a very limited number of sequential NOEs and the absence of any non-sequential NOEs suggest that this region of polypeptide chain is highly flexible. The latter coupled with the occurrence of a large number of basic residues (four out of seven) in the linker region suggests that it may serve to allow adaptable positioning of the nucleic acid recognition sequences within the protein.