PDBsum entry: 2gon

Viral protein

PDB id: 2gon

Contents

Protein chains

127 a.a.

137 a.a.

138 a.a.

Ligands

FLC ×2

Waters ×225

PDB id:

2gon

Name:

Viral protein

Title:

Xray structure of gag133-278

Structure:

Capsid protein p24 (ca). Chain: a, b, c, d. Fragment: n-terminal domain (residues 133-278). Engineered: yes. Mutation: yes

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: isolate new york-5. Gene: gag. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.205 R-free: 0.257

Authors:

B.N.Kelly

Key ref:

B.N.Kelly et al. (2006). Implications for viral capsid assembly from crystal structures of HIV-1 Gag(1-278) and CA(N)(133-278). Biochemistry, 45, 11257-11266. PubMed id: 16981686 DOI: 10.1021/bi060927x

Date:

13-Apr-06 Release date: 26-Sep-06

Protein chains

P12497  (POL_HV1N5) -  Gag-Pol polyprotein

Seq: 1435 a.a.

Struc: 127 a.a.

Protein chain

P12497  (POL_HV1N5) -  Gag-Pol polyprotein

Seq: 1435 a.a.

Struc: 137 a.a.*

Protein chain

P12497  (POL_HV1N5) -  Gag-Pol polyprotein

Seq: 1435 a.a.

Struc: 138 a.a.

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

Enzyme reactions

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

• Biological process: viral reproduction (1 term)

reference

DOI no: 10.1021/bi060927x

Biochemistry 45:11257-11266 (2006)

PubMed id: 16981686

Implications for viral capsid assembly from crystal structures of HIV-1 Gag(1-278) and CA(N)(133-278).

B.N.Kelly, B.R.Howard, H.Wang, H.Robinson, W.I.Sundquist, C.P.Hill.

ABSTRACT

Gag, the major structural protein of retroviruses such as HIV-1, comprises a series of domains connected by flexible linkers. These domains drive viral assembly by mediating multiple interactions between adjacent Gag molecules and by binding to viral genomic RNA and host cell membranes. Upon viral budding, Gag is processed by the viral protease to liberate distinct domains as separate proteins. The first two regions of Gag are MA, a membrane-binding module, and CA, which is a two-domain protein that makes important Gag-Gag interactions, forms the cone-shaped outer shell of the core (the capsid) in the mature HIV-1 particle, and makes an important interaction with the cellular protein cyclophilin A (CypA). Here, we report crystal structures of the mature CA N-terminal domain (CA(N)(133-278)) and a MA-CA(N) fusion (Gag(1-278)) at resolutions/R(free) values of 1.9 A/25.7% and 2.2 A/25.8%, respectively. Consistent with earlier studies, a comparison of these structures indicates that processing at the MA-CA junction causes CA to adopt an N-terminal beta-hairpin conformation that seems to be required for capsid morphology and viral infectivity. In contrast with an NMR study (Tang, C., et al. (2002) Nat. Struct. Biol. 9, 537-543), structural overlap reveals only small relative displacements for helix 6, which is located between the beta-hairpin and the CypA-binding loop. These observations argue against the proposal that CypA binding is coupled with beta-hairpin formation and support an earlier surface plasmon resonance study (Yoo, S., et al. (1997) J. Mol. Biol. 269, 780-795), which concluded that beta-hairpin formation and CypA-binding are energetically independent events.