PDBsum entry 2kod

Viral protein

PDB id: 2kod

Contents

Protein chains

88 a.a.

PDB id:

2kod

Name:

Viral protein

Title:

A high-resolution nmr structure of the dimeric c-terminal domain of HIV-1 ca

Structure:

HIV-1 ca c-terminal domain. Chain: a, b. Engineered: yes

Source:

HIV-1 m:b_hxb2r. HIV-1. Organism_taxid: 11706. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

30 models

Authors:

I.-J.L.Byeon,J.Jung,J.Ahn,J.Concel,A.M.Gronenborn

Key ref:

I.J.Byeon et al. (2009). Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function. Cell, 139, 780-790. PubMed id: 19914170

Date:

18-Sep-09 Release date: 24-Nov-09

Protein chains

P04585  (POL_HV1H2) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)

Seq: 1435 a.a.

Struc: 88 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.- - ?????
• Enzyme class 2: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: E.C.3.1.-.-
• Enzyme class 5: 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 6: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 7: 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

reference

Cell 139:780-790 (2009)

PubMed id: 19914170

Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function.

I.J.Byeon, X.Meng, J.Jung, G.Zhao, R.Yang, J.Ahn, J.Shi, J.Concel, C.Aiken, P.Zhang, A.M.Gronenborn.

ABSTRACT

Mature HIV-1 particles contain conical-shaped capsids that enclose the viral RNA genome and perform essential functions in the virus life cycle. Previous structural analysis of two- and three-dimensional arrays of the capsid protein (CA) hexamer revealed three interfaces. Here, we present a cryoEM study of a tubular assembly of CA and a high-resolution NMR structure of the CA C-terminal domain (CTD) dimer. In the solution dimer structure, the monomers exhibit different relative orientations compared to previous X-ray structures. The solution structure fits well into the EM density map, suggesting that the dimer interface is retained in the assembled CA. We also identified a CTD-CTD interface at the local three-fold axis in the cryoEM map and confirmed its functional importance by mutagenesis. In the tubular assembly, CA intermolecular interfaces vary slightly, accommodating the asymmetry present in tubes. This provides the necessary plasticity to allow for controlled virus capsid dis/assembly.