PDBsum entry: 2e1x

Viral protein

PDB id: 2e1x

Contents

Protein chain

27 a.a.

Metals

_ZN

PDB id:

2e1x

Name:

Viral protein

Title:

Nmr structure of the HIV-2 nucleocapsid protein

Structure:

Gag-pol polyprotein (pr160gag-pol). Chain: a. Fragment: nucleocapsid protein p7, residues 23-49. Synonym: HIV-2 nucleocapsid protein. Engineered: yes

Source:

Synthetic: yes. Other_details: this peptide has been chemically synthesized. This sequence occurs naturally in HIV-2.

NMR struc:

12 models

Authors:

T.Matsui,Y.Kodera,E.Miyauchi,H.Tanaka,H.Endoh,H.Komatsu, T.Tanaka,T.Kohno,T.Maeda

Key ref:

T.Matsui et al. (2007). Structural role of the secondary active domain of HIV-2 NCp8 in multi-functionality. Biochem Biophys Res Commun, 358, 673-678. PubMed id: 17511966 DOI: 10.1016/j.bbrc.2007.04.141

Date:

03-Nov-06 Release date: 05-Jun-07

Protein chain

P18042  (POL_HV2G1) -  Gag-Pol polyprotein

Seq: 1464 a.a.

Struc: 27 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
• Enzyme class 2: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
• Enzyme class 3: 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: E.C.3.1.26.13 - Retroviral ribonuclease H.
• Enzyme class 5: E.C.3.4.23.47 - HIV-2 retropepsin.

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/j.bbrc.2007.04.141

Biochem Biophys Res Commun 358:673-678 (2007)

PubMed id: 17511966

Structural role of the secondary active domain of HIV-2 NCp8 in multi-functionality.

T.Matsui, Y.Kodera, E.Miyauchi, H.Tanaka, H.Endoh, H.Komatsu, T.Tanaka, T.Kohno, T.Maeda.

ABSTRACT

Nucleocapsid protein of HIV, containing two CCHC-type zinc fingers connected by a linker, is a multi-functional protein involved in many critical steps of the HIV life cycle. Several in vitro investigations demonstrated that the reactivities of the first zinc finger flanked by the linker of HIV-1 NCp7 and HIV-2 NCp8 were essential for binding to viral RNA, however, that of the second zinc finger flanked by the linker of NCp7 was very weak and non-specific, whereas the part of NCp8 called NCp8-f2, interacted strongly and specifically with viral RNA. In this study, the three-dimensional structure of NCp8-f2 was determined for the first time. Furthermore, we established that NCp8-f2 specifically binds to the stem-loop SD in viral RNA, and that the hydrophobic cleft and the basic residues close to the cleft were essential for specific binding to SD. We discuss the functional significance of NCp8-f2 for NCp8 being a multi-functional protein.