PDBsum entry 1vse

Endoribonuclease

PDB id: 1vse

Contents

Protein chain

146 a.a. *

Ligands

EPE

Waters ×124

* Residue conservation analysis

PDB id:

1vse

Name:

Endoribonuclease

Title:

Asv integrase core domain with mg(ii) cofactor and hepes ligand, low mg concentration form

Structure:

Integrase. Chain: a. Fragment: catalytic core domain, residues 1 - 4, 52 - 209. Engineered: yes. Other_details: crystals soaked in 20 millimoilar mgcl2

Source:

Rous sarcoma virus (strain schmidt-ruppin). Organism_taxid: 11889. Strain: schmidt-ruppin. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: original viral DNA clone\: ju et al., J. Virol. 33:1026-1033 (1980), original expression clone\: terry et al., J. Virol. 62:2358-2365 (1988), expression clone for core\: kulkosky et al., J. Virol. 206:448-456 (1995)

Biol. unit:

Dimer (from PDB file)

Resolution:

2.20Å R-factor: 0.138 R-free: 0.201

Authors:

G.Bujacz,M.Jaskolski,J.Alexandratos,A.Wlodawer

Key ref:

G.Bujacz et al. (1996). The catalytic domain of avian sarcoma virus integrase: conformation of the active-site residues in the presence of divalent cations. Structure, 4, 89-96. PubMed id: 8805516 DOI: 10.1016/S0969-2126(96)00012-3

Date:

29-Nov-95 Release date: 03-Apr-96

Protein chain

O92956  (POL_RSVSB) -  Gag-Pol polyprotein from Rous sarcoma virus subgroup B (strain Schmidt-Ruppin)

Seq: 1603 a.a.

Struc: 146 a.a.*

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

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.- - ?????
• Enzyme class 3: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 5: E.C.3.1.-.-
• Enzyme class 6: E.C.3.1.26.4 - ribonuclease H.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.
• Enzyme class 7: E.C.3.4.23.- - ?????

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

DOI no: 10.1016/S0969-2126(96)00012-3

Structure 4:89-96 (1996)

PubMed id: 8805516

The catalytic domain of avian sarcoma virus integrase: conformation of the active-site residues in the presence of divalent cations.

G.Bujacz, M.Jaskólski, J.Alexandratos, A.Wlodawer, G.Merkel, R.A.Katz, A.M.Skalka.

ABSTRACT

BACKGROUND: Members of the structurally-related superfamily of enzymes that includes RNase H, RuvC resolvase, MuA transposase, and retroviral integrase require divalent cations for enzymatic activity. So far, cation positions are reported in the X-ray crystal structures of only two of these proteins, E. coli and human immunodeficiency virus 1 (HIV-1) RNase H. Details of the placement of metal ions in the active site of retroviral integrases are necessary for the understanding of the catalytic mechanism of these enzymes. RESULTS: The structure of the enzymatically active catalytic domain (residues 52-207) of avian sarcoma virus integrase (ASV IN) has been solved in the presence of divalent cations (Mn2+ or Mg2+), at 1.7-2.2 A resolution. A single ion of either type interacts with the carboxylate groups of the active site aspartates and uses four water molecules to complete its octahedral coordination. The placement of the aspartate side chains and metal ions is very similar to that observed in the RNase H members of this superfamily; however, the conformation of the catalytic aspartates in the active site of ASV IN differs significantly from that reported for the analogous residues in HIV-1 IN. CONCLUSIONS: Binding of the required metal ions does not lead to significant structural modifications in the active site of the catalytic domain of ASV IN. This indicates that at least one metal-binding site is preformed in the structure, and suggests that the observed constellation of the acidic residues represents a catalytically competent active site. Only a single divalent cation was observed even at extremely high concentrations of the metals. We conclude that either only one metal ion is needed for catalysis, or that a second metal-binding site can only exist in the presence of substrate and/or other domains of the protein. The unexpected differences between the active sites of ASV IN and HIV-1 IN remain unexplained; they may reflect the effects of crystal contacts on the active site of HIV-1 IN, or a tendency for structural polymorphism.

Selected figure(s)

Figure 1.
Figure 1. Chain tracing of the catalytic domain of ASV IN, showing the secondary structure elements and the location of the active site. Figure 1. Chain tracing of the catalytic domain of ASV IN, showing the secondary structure elements and the location of the active site. (Figure prepared using the program RIBBONS [[3]33].)

Figure 2.
Figure 2. Active site of the catalytic domain of ASV IN. (a) Stereoview of the electron-density map (generated using O [34]) for the Mg^2+ complex (500 mM MgCl[2], see text). This F[o]–F[c] map, contoured at 5σ level, was calculated at 1.8 å resolution after refinement of a model which excluded the Mg^2+ cation and its coordinated water molecules. The density corresponding to the cluster of an octahedrally-coordinated metal ion and four waters is exceedingly clear. (b) Stereoview of the active site of ASV IN generated using MOLSCRIPT [35]. Shown is part of the active site displaying the coordination of Mn^2+ with four water molecules, as well as with the carboxylates of Asp121 and Asp64. The water molecule marked W324 is found in the same location in all ASV IN structures. The putative hydrogen bonds made by this molecule (red dashed lines), identified by an analysis of distances and angles, form a distorted tetrahedron (also including a bond to Nε2 of Gln153, not marked). Figure 2. Active site of the catalytic domain of ASV IN. (a) Stereoview of the electron-density map (generated using O [[4]34]) for the Mg^2+ complex (500 mM MgCl[2], see text). This F[o]–F[c] map, contoured at 5σ level, was calculated at 1.8 å resolution after refinement of a model which excluded the Mg^2+ cation and its coordinated water molecules. The density corresponding to the cluster of an octahedrally-coordinated metal ion and four waters is exceedingly clear. (b) Stereoview of the active site of ASV IN generated using MOLSCRIPT [[5]35]. Shown is part of the active site displaying the coordination of Mn^2+ with four water molecules, as well as with the carboxylates of Asp121 and Asp64. The water molecule marked W324 is found in the same location in all ASV IN structures. The putative hydrogen bonds made by this molecule (red dashed lines), identified by an analysis of distances and angles, form a distorted tetrahedron (also including a bond to Nε2 of Gln153, not marked).

The above figures are reprinted by permission from Cell Press: Structure (1996, 4, 89-96) copyright 1996.

Figures were selected by an automated process.