PDBsum entry 2fqv

Hydrolase

PDB id: 2fqv

Contents

Protein chains

163 a.a.

87 a.a.

Ligands

F2G

Waters ×183

Superseded by:

2hbz

PDB id:

2fqv

Name:

Hydrolase

Title:

Crystal structure of human caspase-1 (arg286->ala, glu390- >ala) in complex with 3-[2-(2-benzyloxycarbonylamino-3- methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-vad-fmk)

Structure:

Caspase-1. Chain: a. Fragment: p20 subunit, residues 120-297. Engineered: yes. Mutation: yes. Caspase-1. Chain: b. Fragment: p10 subunit, residues 317-404. Engineered: yes.

Source:

Homo sapiens. Human. Gene: casp1, il1bc, il1bce. Expressed in: escherichia coli.

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.90Å R-factor: 0.225 R-free: 0.249

Authors:

J.M.Scheer,J.A.Wells,M.J.Romanowski

Key ref:

J.M.Scheer et al. (2006). A common allosteric site and mechanism in caspases. Proc Natl Acad Sci U S A, 103, 7595-7600. PubMed id: 16682620 DOI: 10.1073/pnas.0602571103

Date:

18-Jan-06 Release date: 16-May-06

Protein chain

P29466  (CASP1_HUMAN) -  Caspase-1 from Homo sapiens

Seq: 404 a.a.

Struc: 163 a.a.*

Protein chain

P29466  (CASP1_HUMAN) -  Caspase-1 from Homo sapiens

Seq: 404 a.a.

Struc: 87 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.3.4.22.36 - caspase-1.
• Reaction: Release of interleukin 1-beta by specific cleavage at 116-Asp-|-Ala-117 and 27-Asp-|-Gly-28 bonds in precursor. Also hydrolyzes the small- molecule substrate, Ac-Tyr-Val-Ala-Asp-|-NHMec.

DOI no: 10.1073/pnas.0602571103

Proc Natl Acad Sci U S A 103:7595-7600 (2006)

PubMed id: 16682620

A common allosteric site and mechanism in caspases.

J.M.Scheer, M.J.Romanowski, J.A.Wells.

ABSTRACT

We present a common allosteric mechanism for control of inflammatory and apoptotic caspases. Highly specific thiol-containing inhibitors of the human inflammatory caspase-1 were identified by using disulfide trapping, a method for site-directed small-molecule discovery. These compounds became trapped by forming a disulfide bond with a cysteine residue in the cavity at the dimer interface approximately 15 A away from the active site. Mutational and structural analysis uncovered a linear circuit of functional residues that runs from one active site through the allosteric cavity and into the second active site. Kinetic analysis revealed robust positive cooperativity not seen in other endopeptidases. Recently, disulfide trapping identified a similar small-molecule site and allosteric transition in the apoptotic caspase-7 that shares only a 23% sequence identity with caspase-1. Together, these studies show a general small-molecule-binding site for functionally reversing the zymogen activation of caspases and suggest a common regulatory site for the allosteric control of inflammation and apoptosis.

Selected figure(s)

Figure 1.
Fig. 1. Structure of an allosteric inhibitor bound to caspase-1. (a) 2F[o] - F[c] electron density for Compound 34 used for compound model building, contoured at 1 , is shown as a blue mesh at the dimer interface (PDB ID code 2FQQ). (b) Two molecules of Compound 34 are shown as spheres in the central cavity at the dimer interface of caspase-1. (c) Residues involved in forming the binding pocket for Compound 34 are shown as spheres. Residues from the large subunit (Glu-241, Gln-257, and Arg-286) are colored blue, and residues from the small subunit (Thr-388, Glu-390, and Arg-391) are colored tan. (d) Residues likely involved in the mechanism of inhibition of caspase-1 by allosteric compounds are displayed. Arg-286 adjacent to the catalytic Cys-285 is located >12 Å from Glu-390, to which it is salt-bridged in the active conformation. The amide nitrogen of the linker group of Compound 34 is within a hydrogen-bonding distance of the Glu-390 carboxylate. Arg-391 is shown to indicate the boundary of the binding pocket.

Figure 3.
Fig. 3. Structural analysis of mutations in the allosteric circuit of caspase-1. (a) A network of interactions across the dimer interface of caspase-1 in the z-VAD-FMK-inhibited protein. The inhibitor is shown as yellow sticks in the upper left and lower right. The active-site Cys-285 and Arg-286 are displayed as blue sticks, Glu-390 at the dimer interface as tan sticks, and a water molecule mediating the interaction between the two Glu residues is shown as a red sphere. (b) The x-ray crystal structure of each allosteric-circuit mutant was determined in the presence of the active-site inhibitor z-VAD-FMK. All structures (PDB ID codes 2FQS, R286A; 2FQU, E390A; and 2FQV, R286A/E390A) adopted a dimeric structure very similar to that of the wild-type enzyme in complex with an active-site inhibitor (PDB ID code 2FQR). No significant conformational changes were observed in the enzymes except for those involving residues in the allosteric circuit. The 2F[o] - F[c] electron density for residues Arg-286, Glu-390, and Thr-388 is displayed. (Bottom Left) The position of Compound 34 displayed as spheres. (Bottom Right) The ligand-free (apo) conformation of caspase-1.

Figures were selected by the author.