PDBsum entry 1jq7

Hydrolase/hydrolase inhibitor

PDB id: 1jq7

Contents

Protein chains

210 a.a. *

217 a.a. *

Ligands

0FP ×2

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Molecular mechanism for dimerization to regulate the catalytic activity of human cytomegalovirus protease.

Authors

R.Batra, R.Khayat, L.Tong.

Ref.

Nat Struct Biol, 2001, 8, 810-817. [DOI no: 10.1038/nsb0901-810]

PubMed id

11524687

Abstract

Biochemical studies indicate that dimerization is required for the catalytic activity of herpesvirus proteases, whereas structural studies show a complete active site in each monomer, away from the dimer interface. Here we report kinetic, biophysical and crystallographic characterizations of structure-based mutants in the dimer interface of human cytomegalovirus (HCMV) protease. Such mutations can produce a 1,700-fold reduction in the kcat while having minimal effects on the K(m). Dimer stability is not affected by these mutations, suggesting that dimerization itself is insufficient for activity. There are large changes in monomer conformation and dimer organization of the apo S225Y mutant enzyme. However, binding of an activated peptidomimetic inhibitor induced a conformation remarkably similar to the wild type protease. Our studies suggest that appropriate dimer formation may be required to indirectly stabilize the protease oxyanion hole, revealing a novel mechanism for dimerization to regulate enzyme activity.

Figure 3.
Figure 3. Crystal structure of the free enzyme of the S225Y mutant of HCMV protease. a, The structure of the monomer of the S225Y mutant, produced with RIBBONS27. Some of the secondary structure elements that show differences to the wild type structure are labeled. The side chain of Tyr 225 is shown in green. b, Superposition of the structures of HCMV protease wild type (yellow) and the S225Y mutant (cyan). Regions of large conformational differences between the two structures are labeled with the names of the secondary structure elements. The side chains of Arg 165 and Arg 166 in the wild type structure are shown in purple. c, Schematic drawing showing the dimer of the S225Y mutant, produced with RIBBONS27. The Tyr 225 side chains are shown in green. d, Superposition of the dimers of wild type (yellow) and S225Y mutant (cyan). The monomer on the left was superimposed, and only the structure of the wild type is shown. A 26° rotation, around the direction indicated by the bar, is needed to bring the other monomer into overlap. Produced with GRASP28. e, Stereo view of the final 2F[O] - F[c] electron density for residues 217 -230 in helix F at 2.3 Å resolution, contoured at 1 . Produced with SETOR29.

Figure 5.
Figure 5. Crystal structure of the S225Y mutant in complex with the inhibitor BILC 408. a, Chemical structure of the BILC 408 inhibitor. b, Superposition of the dimer of HCMV protease wild type (yellow) and the S225Y mutant in complex with BILC 408 (cyan). The inhibitor is shown in green for carbon atoms. The side chains of residue 225 and the active site are also shown. Produced with RIBBONS27. c, Molecular surface of the active site region of the S225Y mutant in complex with BILC 408. There is a gap in one side of the S[3] pocket, due to the absence of the Arg 137 side chain. Produced with GRASP28.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 810-817) copyright 2001.