PDBsum entry 2ow2

Hydrolase/hydrolase inhibitor

PDB id: 2ow2

Contents

Protein chain

156 a.a. *

Ligands

8MR ×2

Metals

_ZN ×4

_CA ×6

_CL ×2

Waters ×117

* Residue conservation analysis

PDB id:

2ow2

Name:

Hydrolase/hydrolase inhibitor

Title:

Mmp-9 active site mutant with difluoro butanoic acid inhibitor

Structure:

Matrix metalloproteinase-9 (mmp-9) (92 kda type iv collagenase) (92 kda gelatinase) (gelatinase b) (gelb). Chain: a, b. Fragment: catalytic domain residues: 110-215, 391-443. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: mmp9, clg4b. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.90Å R-factor: 0.215 R-free: 0.285

Authors:

A.Tochowicz,W.Bode,K.Maskos,P.Goettig

Key ref:

A.Tochowicz et al. (2007). Crystal structures of MMP-9 complexes with five inhibitors: contribution of the flexible Arg424 side-chain to selectivity. J Mol Biol, 371, 989. PubMed id: 17599356 DOI: 10.1016/j.jmb.2007.05.068

Date:

15-Feb-07 Release date: 19-Jun-07

Protein chains

P14780  (MMP9_HUMAN) -  Matrix metalloproteinase-9 from Homo sapiens

Seq: 707 a.a.

Struc: 156 a.a.*

* PDB and UniProt seqs differ at 46 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.24.35 - gelatinase B.
• Reaction: Cleavage of gelatin types I and V and collagen types IV and V.
• Cofactor: Ca(2+); Zn(2+)

DOI no: 10.1016/j.jmb.2007.05.068

J Mol Biol 371:989 (2007)

PubMed id: 17599356

Crystal structures of MMP-9 complexes with five inhibitors: contribution of the flexible Arg424 side-chain to selectivity.

A.Tochowicz, K.Maskos, R.Huber, R.Oltenfreiter, V.Dive, A.Yiotakis, M.Zanda, W.Bode, P.Goettig.

ABSTRACT

Human matrix metalloproteinase 9 (MMP-9), also called gelatinase B, is particularly involved in inflammatory processes, bone remodelling and wound healing, but is also implicated in pathological processes such as rheumatoid arthritis, atherosclerosis, tumour growth, and metastasis. We have prepared the inactive E402Q mutant of the truncated catalytic domain of human MMP-9 and co-crystallized it with active site-directed synthetic inhibitors of different binding types. Here, we present the X-ray structures of five MMP-9 complexes with gelatinase-specific, tight binding inhibitors: a phosphinic acid (AM-409), a pyrimidine-2,4,6-trione (RO-206-0222), two carboxylate (An-1 and MJ-24), and a trifluoromethyl hydroxamic acid inhibitor (MS-560). These compounds bind by making a compromise between optimal coordination of the catalytic zinc, favourable hydrogen bond formation in the active-site cleft, and accommodation of their large hydrophobic P1' groups in the slightly flexible S1' cavity, which exhibits distinct rotational conformations of the Pro421 carbonyl group in each complex. In all these structures, the side-chain of Arg424 located at the bottom of the S1' cavity is not defined in the electron density beyond C(gamma), indicating its mobility. However, we suggest that the mobile Arg424 side-chain partially blocks the S1' cavity, which might explain the weaker binding of most inhibitors with a long P1' side-chain for MMP-9 compared with the closely related MMP-2 (gelatinase A), which exhibits a short threonine side-chain at the equivalent position. These novel structural details should facilitate the design of more selective MMP-9 inhibitors.

Selected figure(s)

Figure 2.
Figure 2. Complex of mini-MMP-9 and the phosphinic acid inhibitor AM-409 ([2-[1-carbamoyl-2-(1H-Indol-3-yl)-ethylcarbamoyl]-3-(3-phenyl-isoxazol-5-yl)-propyl]-phenyl-phosphinic acid). (a) Chemical formula of AM-409 and K[i] values against several MMPs (V.D., unpublished results). (b) Stereo plot of a section around the active site of mini-MMP-9 in standard orientation (see Figure 1(a)), superimposed with the 2F[obs]–F[calc] electron density (orange) accounting for the inhibitor, contoured at 1σ. The inhibitor and the mini-MMP-9 are shown as stick models, with nitrogen and oxygen atoms in blue and red, and carbon atoms in yellow and green, respectively. The phosphorus atom is depicted in dark grey. Ionic bonds to the catalytic zinc and intermolecular hydrogen bonds are shown as broken lines (distances in Å). Water molecules are displayed as blue spheres. Only the dominating of two AM-409 conformations is depicted.

Figure 3.
Figure 3. Complex of mini-MMP-9 and the barbiturate inhibitor RO-206-0222 (5-(4-phenoxy-phenyl)-5-(4-pyrimidin-2-yl-piperazin-1-yl)-pyrimidin-2,4,6-trione). (a) Chemical formula of RO-206-0222 and IC[50] values against several MMPs.^32 (b) Stereo representation of the active site region of mini-MMP-9-RO-206-0222, superimposed with the 2F[obs]–F[calc] electron density (orange) around the inhibitor, contoured at 1σ. The standard orientation is as in Figure 1(a). The inhibitor and the mini-MMP-9 are shown as stick models, with nitrogen and oxygen atoms in blue and red, and carbon atoms in yellow and green, respectively. Ionic bonds to the catalytic zinc and intermolecular hydrogen bonds are shown as broken lines (distances in Å).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 371, 989-0) copyright 2007.

Figures were selected by an automated process.