PDBsum entry: 1cl4

Viral protein

PDB id: 1cl4

Contents

Protein chain

32 a.a. *

Metals

_ZN

* Residue conservation analysis

PDB id:

1cl4

Name:

Viral protein

Title:

Nucleocapsid protein from mason-pfizer monkey virus (mpmv)

Structure:

Protein (gag polyprotein). Chain: a. Fragment: gag residues 574-605 (p14 residues 49-80). Engineered: yes. Mutation: yes

Source:

Mason-pfizer monkey virus. Organism_taxid: 11855. Gene: ncp14. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

12 models

Authors:

Y.Gao,K.Kaluarachchi,D.P.Giedroc

Key ref:

Y.Gao et al. (1998). Solution structure and backbone dynamics of Mason-Pfizer monkey virus (MPMV) nucleocapsid protein. Protein Sci, 7, 2265-2280. PubMed id: 9827993 Ref: Full text

Date:

06-May-99 Release date: 11-May-99

Protein chain

P07567  (GAG_MPMV) -  Gag polyprotein

Seq: 657 a.a.

Struc: 32 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (2 terms)

Full text	Protein Sci 7:2265-2280 (1998)
PubMed id: 9827993

Solution structure and backbone dynamics of Mason-Pfizer monkey virus (MPMV) nucleocapsid protein.

Y.Gao, K.Kaluarachchi, D.P.Giedroc.

ABSTRACT

Retroviral nucleocapsid proteins (NCPs) are CCHC-type zinc finger proteins that mediate virion RNA binding activities associated with retrovirus assembly and genomic RNA encapsidation. Mason-Pfizer monkey virus (MPMV), a type D retrovirus, encodes a 96-amino acid nucleocapsid protein, which contains two Cys-X2-Cys-X4-His-X4-Cys (CCHC) zinc fingers connected by an unusually long 15-amino acid linker. Homonuclear, two-dimensional sensitivity-enhanced 15N-1H, three-dimensional 15N-1H, and triple resonance NMR spectroscopy have been used to determine the solution structure and residue-specific backbone dynamics of the structured core domain of MPMV NCP containing residues 21-80. Structure calculations and spectral density mapping of N-H bond vector mobility reveal that MPMV NCP 21-80 is best described as two independently folded, rotationally uncorrelated globular domains connected by a seven-residue flexible linker consisting of residues 42-48. The N-terminal CCHC zinc finger domain (residues 24-37) appears to adopt a fold like that described previously for HIV-1 NCP; however, residues within this domain and the immediately adjacent linker region (residues 38-41) are characterized by extensive conformational averaging on the micros-ms time scale at 25 degrees C. In contrast to other NCPs, residues 49-77, which includes the C-terminal CCHC zinc-finger (residues 53-66), comprise a well-folded globular domain with the Val49-Pro-Gly-Leu52 sequence and C-terminal tail residues 67-77 characterized by amide proton exchange properties and 15N R1, R2, and (1H-15N) NOE values indistinguishable to residues in the core C-terminal finger. Twelve refined structural models of MPMV NCP residues 49-80 (pairwise backbone RMSD of 0.77 A) reveal that the side chains of the conserved Pro50 and Trp62 are in van der Waals contact with one another. Residues 70-73 in the C-terminal tail adopt a reverse turn-like structure. Ile77 is involved in extensive van der Waals contact with the core finger domain, while the side chains of Ser68 and Asn75 appear to form hydrogen bonds that stabilize the overall fold of this domain. These residues outside of the core finger structure are conserved in D-type and related retroviral NCPs, e.g., MMTV NCP, suggesting that the structure of MPMV NCP may be representative of this subclass of retroviral NCPs.

Selected figure(s)

Figure 4.
Fig. 4. Superposition of12lowestenergy structures ofNCP21-80residues49-80. The backbone atoms of residues 4-77 wereused to define the limits of the superposition. The backboneatomsofallresidues are showningraywith conserved side colored. Green are hydrophobic (Proso, Trp2, Leu52, Pro76, Ile77); Cys are in yellow;His61isblue;polaranduncharged Ser68 and Asn75arered. These structures superimposeresidues49-77withan average RMSD of 0.77 A for the backboneatomsand1.36 A for allatoms. The conformation oftheNterminalCCHCzinc-fingerisnotwell defined by the data. Figure created witSPOCK (Christopher,1998)andrenderedwithRaster3D (Bacon & Anderson,1988; Memtt & Murphy, 1994).

Figure 5.
Fig. 5. Ribbonrepresentationofabackbonesuperposition ofHIV-INCP F1 (Summers et al., 990)with MPMVNCP C-termnal domainTheaminoacidsequence oftheHIV-1F1 peptideis Vall-Lys2-Cys3-Phe4-Asn5-Cys6-Gly7-Lys8-Glu9-GlylO-~sll-~el2- Alal3-Lysl4-AsnlS-Cys16-Arg17-Alal8 (Summerset al., 1990). The14aminoacidzinc-fingermotifdefinesthelimits ofthe superposition(residues 3-16inHIV-1NCPand53-66 in MPMV NCP).Notethesignificantdifferencesinpolypeptidechaintrajectory betweenthesecondandthirdzincligandsbetween the twomolecules.FigurecreatedwithSPOCK(Christopher,1998).

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1998, 7, 2265-2280) copyright 1998.

Figures were selected by an automated process.