PDBsum entry: 2pc0

Hydrolase

PDB-id: 2pc0

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PROCHECK

Protein chain

99 a.a. *

Ligands

PGR

Metal ions

_MG

Waters ×112

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

2pc0

Name:

Hydrolase

Title:

Apo wild-type HIV protease in the open conformation

Structure:

Protease. Chain: a. Engineered: yes. Mutation: yes

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: bh10. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

A3FH86 (A3FH86_9HIV1)

Seq:

99 a.a.

Struc:

99 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

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

Resolution:

1.40Å

R-factor:

0.155

R-free:

0.186

Authors:

H.Heaslet,R.Rosenfeld,M.J.Giffin,J.H.Elder,D.E.Mcree, C.D.Stout

Key ref:

H.Heaslet et al. (2007). Conformational flexibility in the flap domains of ligand-free HIV protease.. Acta Crystallogr D Biol Crystallogr, 63, 866-875. [PubMed id: 17642513] [DOI: 10.1107/S0907444907029125]

Date:

29-Mar-07

Release date:

26-Jun-07

Related entries:

2hb4
apo wild-type HIV protease in the curled conformation.
2hb2
apo 6x mutant HIV protease in the curled conformation.
2az8
wild-type HIV protease in complex with tl-3.

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Clefts

Surface

Key reference

DOI no: 10.1107/S0907444907029125

Acta Crystallogr D Biol Crystallogr 63:866-875 (2007)

PubMed id: 17642513

Conformational flexibility in the flap domains of ligand-free HIV protease.

H.Heaslet, R.Rosenfeld, M.Giffin, Y.C.Lin, K.Tam, B.E.Torbett, J.H.Elder, D.E.McRee, C.D.Stout.

ABSTRACT

The crystal structures of wild-type HIV protease (HIV PR) in the absence of substrate or inhibitor in two related crystal forms at 1.4 and 2.15 A resolution are reported. In one crystal form HIV PR adopts an 'open' conformation with a 7.7 A separation between the tips of the flaps in the homodimer. In the other crystal form the tips of the flaps are 'curled' towards the 80s loop, forming contacts across the local twofold axis. The 2.3 A resolution crystal structure of a sixfold mutant of HIV PR in the absence of substrate or inhibitor is also reported. The mutant HIV PR, which evolved in response to treatment with the potent inhibitor TL-3, contains six point mutations relative to the wild-type enzyme (L24I, M46I, F53L, L63P, V77I, V82A). In this structure the flaps also adopt a 'curled' conformation, but are separated and not in contact. Comparison of the apo structures to those with TL-3 bound demonstrates the extent of conformational change induced by inhibitor binding, which includes reorganization of the packing between twofold-related flaps. Further comparison with six other apo HIV PR structures reveals that the 'open' and 'curled' conformations define two distinct families in HIV PR. These conformational states include hinge motion of residues at either end of the flaps, opening and closing the entire beta-loop, and translational motion of the flap normal to the dimer twofold axis and relative to the 80s loop. The alternate conformations also entail changes in the beta-turn at the tip of the flap. These observations provide insight into the plasticity of the flap domains, the nature of their motions and their critical role in binding substrates and inhibitors.

Selected figure(s)

Figure 3.
Figure 3 Flap conformational changes induced by binding of TL-3 to wild-type HIV PR. In the absence of substrate or inhibitor, the flap regions of wild-type HIV PR adopt two distinct conformations: `open' (rose) and `curled' (green). While the flap regions lack interactions in the `open' conformation, a stabilizing packing interaction is formed between the side chains of Phe53 and Ile50' of twofold-related monomers in the `curled' conformation. Upon binding of TL-3 (cyan), the flaps shift toward the active site and their interactions are reconfigured: the side chain of Phe53 now interacts with the P4 benzyl group of TL-3 (light blue) and Ile50 contacts Ile54'. TL-3 also induces a shift in the 80s loop, which moves towards the inhibitor such that Pro81' and Val82' contact the P1 benzyl group.

Figure 4.
Figure 4 Expanded `curled' flap conformation in the 2.3 Å structure of apo 6× HIV PR: view of the flaps, 80s loop and active site of the unliganded 6× HIV PR showing the expanded `curled' configuration of the flaps. As in the `curled' conformation of wild-type HIV PR, the flaps of 6× HIV PR adopt the `top-to-top' orientation, but are 5 Å farther apart and lack stabilizing interactions. The flap residues Gly48 and Gly49 are disordered, along with the side chain of Ile50. The further expansion shifts the flaps toward the 80s loop, allowing a packing contact between Ile50 and Pro81 in the same subunit. The active site is devoid of ordered water molecules or metal ions.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 866-875) copyright 2007.

Figures were selected by an automated process.