PDBsum entry 1vsk

Hydrolase

PDB id: 1vsk

Contents

Protein chain

146 a.a. *

Waters ×106

* Residue conservation analysis

PDB id:

1vsk

Name:

Hydrolase

Title:

Asv integrase core domain d64n mutation in citrate buffer ph 6.0

Structure:

Integrase. Chain: a. Fragment: catalytic core domain. Engineered: yes. Mutation: yes. Other_details: p03354 fragment of polyprotein pol-rsvp

Source:

Rous sarcoma virus - schmidt-ruppin b. Organism_taxid: 269447. Strain: schmidt-ruppin b. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.20Å R-factor: 0.159 R-free: 0.249

Authors:

J.Lubkowski,F.Yang,J.Alexandratos,A.Wlodawer

Key ref:

J.Lubkowski et al. (1998). Structural basis for inactivating mutations and pH-dependent activity of avian sarcoma virus integrase. J Biol Chem, 273, 32685-32689. PubMed id: 9830010 DOI: 10.1074/jbc.273.49.32685

Date:

18-Sep-98 Release date: 02-Dec-98

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 2 residue positions (black crosses)

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: 10.1074/jbc.273.49.32685

J Biol Chem 273:32685-32689 (1998)

PubMed id: 9830010

Structural basis for inactivating mutations and pH-dependent activity of avian sarcoma virus integrase.

J.Lubkowski, F.Yang, J.Alexandratos, G.Merkel, R.A.Katz, K.Gravuer, A.M.Skalka, A.Wlodawer.

ABSTRACT

Crystallographic studies of the catalytic core domain of avian sarcoma virus integrase (ASV IN) have provided the most detailed picture so far of the active site of this enzyme, which belongs to an important class of targets for designing drugs against AIDS. Recently, crystals of an inactive D64N mutant were obtained under conditions identical to those used for the native enzyme. Data were collected at different pH values and in the presence of divalent cations. Data were also collected at low pH for the crystals of the native ASV IN core domain. In the structures of native ASV IN at pH 6.0 and below, as well as in all structures of the D64N mutants, the side chain of the active site residue Asx-64 (Asx denotes Asn or Asp) is rotated by approximately 150 degrees around the Calpha---Cbeta bond, compared with the structures at higher pH. In the new structures, this residue makes hydrogen bonds with the amide group of Asn-160, and thus, the usual metal-binding site, consisting of Asp-64, Asp-121, and Glu-157, is disrupted. Surprisingly, however, a single Zn2+ can still bind to Asp-121 in the mutant, without restoration of the activity of the enzyme. These structures have elucidated an unexpected mechanism of inactivation of the enzyme by lowering the pH or by mutation, in which a protonated side chain of Asx-64 changes its orientation and interaction partner.

Selected figure(s)

Figure 1.
Fig. 1. The active site of ASV IN (catalytic core domain). A, F[o] F[c] difference density "omit" map, contoured at 2.5 , showing the position of the side chain of D64N (blue) compared with the side chain of Asp-64 (brown) in the active conformation. The hydrogen bonding pattern of a structurally conserved water molecule observed in all ASV IN structures is also shown. B, hydrogen bonding of the side chain of D64N with Asn-160. The hydrogen bonding pattern of a structurally conserved water molecule observed in all ASV IN structures is also shown. C, hydrogen bonding of the side chain of Asp-64 with the structurally conserved water.

Figure 2.
Fig. 2. The active site of ASV IN (catalytic core domain) with bound zinc cation(s). A, 2F[o] F[c] density map, contoured at 2.5 , showing the bound Zn2+ hydrogen bonded only to the side chain of Asp-121. The side chain of D64N is hydrogen bonded to Asn-160. B, a previously determined structure of ASV IN, showing the bound zinc cations hydrogen bonded to the side chains of Asp-64 and Asp-121.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 32685-32689) copyright 1998.

Figures were selected by the author.