PDBsum entry: 1aaf

Viral protein

PDB-id: 1aaf

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

55 a.a. *

Metal ions

_ZN ×2

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1aaf

Name:

Viral protein

Title:

Nucleocapsid zinc fingers detected in retroviruses: exafs studies on intact viruses and the solution-state structure of the nucleocapsid protein from HIV-1

Structure:

HIV-1 nucleocapsid protein. Chain: a. Engineered: yes

Source:

HIV-1 m:b_mn. Organism_taxid: 11696. Expressed in: escherichia coli. Expression_system_taxid: 562

UniProt:

P05961 (POL_HV1MN)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

1441 a.a.

Struc:

55 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class 1:

E.C.2.7.7.49   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (see diagram below)

Enzyme class 2:

E.C.2.7.7.7   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (see diagram below)

Enzyme class 3:

E.C.3.1.26.4   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Endonucleolytic cleavage to 5'-phosphomonoester.

Enzyme class 4:

E.C.3.4.23.16   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

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.

Resolution:

not givenÅ

NMR structure:

20 models

Authors:

M.F.Summers,L.E.Henderson,M.R.Chance,J.W.Bess Junior, T.L.South,P.R.Blake,I.Sagi,G.Perez-Alvarado,R.C.Sowder, D.R.Hare,L.O.Arthur

Key ref:

M.F.Summers et al. (1992). Nucleocapsid zinc fingers detected in retroviruses: EXAFS studies of intact viruses and the solution-state structure of the nucleocapsid protein from HIV-1.. Protein Sci, 1, 563-574. [PubMed id: 1304355]

Date:

06-Apr-92

Release date:

31-Jan-94

Quick_links

Procheck

Clefts

Surface

Key reference

Full text	Protein Sci 1:563-574 (1992)
PubMed id: 1304355

Nucleocapsid zinc fingers detected in retroviruses: EXAFS studies of intact viruses and the solution-state structure of the nucleocapsid protein from HIV-1.

M.F.Summers, L.E.Henderson, M.R.Chance, J.W.Bess, T.L.South, P.R.Blake, I.Sagi, G.Perez-Alvarado, R.C.Sowder, D.R.Hare.

ABSTRACT

All retroviral nucleocapsid (NC) proteins contain one or two copies of an invariant 3Cys-1His array (CCHC = C-X2-C-X4-H-X4-C; C = Cys, H = His, X = variable amino acid) that are essential for RNA genome packaging and infectivity and have been proposed to function as zinc-binding domains. Although the arrays are capable of binding zinc in vitro, the physiological relevance of zinc coordination has not been firmly established. We have obtained zinc-edge extended X-ray absorption fine structure (EXAFS) spectra for intact retroviruses in order to determine if virus-bound zinc, which is present in quantities nearly stoichiometric with the CCHC arrays (Bess, J.W., Jr., Powell, P.J., Issaq, H.J., Schumack, L.J., Grimes, M.K., Henderson, L.E., & Arthur, L.O., 1992, J. Virol. 66, 840-847), exists in a unique coordination environment. The viral EXAFS spectra obtained are remarkably similar to the spectrum of a model CCHC zinc finger peptide with known 3Cys-1His zinc coordination structure. This finding, combined with other biochemical results, indicates that the majority of the viral zinc is coordinated to the NC CCHC arrays in mature retroviruses. Based on these findings, we have extended our NMR studies of the HIV-1 NC protein and have determined its three-dimensional solution-state structure. The CCHC arrays of HIV-1 NC exist as independently folded, noninteracting domains on a flexible polypeptide chain, with conservatively substituted aromatic residues forming hydrophobic patches on the zinc finger surfaces. These residues are essential for RNA genome recognition, and fluorescence measurements indicate that at least one residue (Trp37) participates directly in binding to nucleic acids in vitro. The NC is only the third HIV-1 protein to be structurally characterized, and the combined EXAFS, structural, and nucleic acid-binding results provide a basis for the rational design of new NC-targeted antiviral agents and vaccines for the control of AIDS.

Selected figure(s)

Figure 5.
Fig. 5. Superpostion of residuesCysl5-CysZ8(bottom)and Cy~~~-Cy ~~(top) of the 3 IV-1 NC DG structures. For clarity, onlythebackboneatoms of residues ys-GlnS3areshown in thefigure.Thisfigureillustratesthefindingthatonlythe CCHC arrays exist in auniquesolution-stateconformation.

Figure 6.
Fig. 6. Structreofthe HIV-1 NC protein displayed as a Ca tube trac- ing of diameter 1 A. The red an blue colors enotethconformtion- allylabileN- and C-terminal tails and linker segments and the structured CCHC finger domains, The figure was rendered on a Silicon Graphics computer with the Ray-T softwarepackage (T. Palmer, Cray Inc.).

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1992, 1, 563-574) copyright 1992.

Figures were selected by an automated process.