PDBsum entry: 1mfs

Viral protein

PDB id: 1mfs

Contents

Protein chain

55 a.a. *

Metals

_ZN ×2

* Residue conservation analysis

PDB id:

1mfs

Name:

Viral protein

Title:

Dynamical behavior of the HIV-1 nucleocapsid protein; nmr, 30 structures

Structure:

HIV-1 nucleocapsid protein. Chain: a. Fragment: nucleocapsid, zinc binding domains. Engineered: yes

Source:

Human immunodeficiency virus. Organism_taxid: 12721. Strain: nl4-3. Cell_line: bl21. Gene: nc. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

30 models

Authors:

M.F.Summers,B.G.Turner,R.N.De Guzman,B.M.Lee,N.Tjandra

Key ref:

B.M.Lee et al. (1998). Dynamical behavior of the HIV-1 nucleocapsid protein. J Mol Biol, 279, 633-649. PubMed id: 9641983 DOI: 10.1006/jmbi.1998.1766

Date:

01-Apr-98 Release date: 17-Jun-98

Protein chain

P35963  (POL_HV1Y2) -  Gag-Pol polyprotein

Seq: 1435 a.a.

Struc: 55 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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.3.4.23.16 - 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: 10.1006/jmbi.1998.1766

J Mol Biol 279:633-649 (1998)

PubMed id: 9641983

Dynamical behavior of the HIV-1 nucleocapsid protein.

B.M.Lee, R.N.De Guzman, B.G.Turner, N.Tjandra, M.F.Summers.

ABSTRACT

The HIV-1 nucleocapsid protein (NC) contains two CCHC-type zinc knuckle domains that are essential for genome recognition, packaging and infectivity. The solution structure of the protein has been determined independently by three groups. Although the structures of the individual zinc knuckle domains are similar, two of the studies indicated that the knuckles behave as independently folded, non-interacting domains connected by a flexible tether, whereas one study revealed the presence of interknuckle NOE cross-peaks, which were interpreted in terms of a more compact structure in which the knuckles are in close proximity. We have collected multidimensional NMR data for the recombinant, isotopically labeled HIV-1 NC protein, and confirmed the presence of weak interknuckle NOEs. However, the NOE data are not consistent with a single protein conformation. 15N NMR relaxation studies reveal that the two zinc knuckle domains possess different effective rotational correlation times, indicating that the knuckles are not tumbling as a single globular domain. In addition, the 1H NMR chemical shifts of isolated zinc knuckle peptides are very similar to those of the intact protein. The combined results indicate that the interknuckle interactions, which involve the close approach of the side-chains of Phe16 and Trp37, are transitory. The solution behavior of NC may be best considered as a rapid equilibrium between conformations with weakly interacting and non-interacting knuckle domains. This inherent conformational flexibility may be functionally important, enabling adaptive binding of NC to different recognition elements within the HIV-1 psi-RNA packaging signal.

Selected figure(s)

Figure 5.
Figure 5. Comparison of the ^15N backbone relaxation NMR data (average values from two experiments) for the N-terminal (shaded rectangles) and C-terminal (open rectangles) CCHC zinc knuckle domains of the HIV-1 NC protein. The N and C-terminal arrays begin at residue Cys15 and Cys36, respectively. Small but significant differences in the T[1]and NOE data indicate that the rotational correlation time of the C-terminal zinc knuckle is smaller than that of the N-terminal zinc knuckle.

Figure 7.
Figure 7. Drawing of the N-terminal domain of the HIV-1 NC protein showing its relationship to the long axis (D[zz]) of the axially symmetric diffusion tensor. Heavy atoms of the side-chains of the zinc-coordinating Cys (yellow) and His (cyan) residues are included. For clarity, the zinc atom is not shown. The relaxation data indicate that the diffusion tensor for the C-terminal zinc knuckle domain (not shown) is isotropic. The Figure was generated with the Midas Plus software package [Ferrin et al 1988].

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 279, 633-649) copyright 1998.

Figures were selected by an automated process.