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MMP8

MMP-8, also called, Neutrophil collagenase or Collagenase 2, is a zinc-dependent and calcium-dependent enzyme. It belongs to the matrix metalloproteinase (MMP) family which is involved in the breakdown of extracellular matrix in embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. The gene coding this family is localized on the chromosome 11 of Homo sapiens .^[1]

1 Classification
2 To see
3 Structure and domains
4 Mechanism
5 Function
6 Disease
7 Relevance
8 Structural highlights

Classification

EC 3.4.24.34 This classification means that this enzyme:

is a hydrolase: it hydrolyzes covalent bonds
is an endopeptidase: it cleaves peptide bond
cleaves interstitial collagens in the triple helical domain (at a site about three-fourths away from the N-terminus)

The difference between this classification and EC 3.4.24.7 is that this enzyme cleaves type III collagen more slowly than type I.

To see

[1] [2] ^[2] [3] [4] pockets [5]

Structure and domains

MMP8 is composed of several domains: a propeptide, a catalytic domain, a hinge region, and a C-terminal hemopexinlike domain.^[3]

Propeptide

It corresponds to , from Phe21 to Met100. The sequence of residue is: FPVSSKEKNTKTVQDYLEKFYQLPSNQYQSTRKNGTNVIVEKLKEMQRFFGLNVTGKPNEETLDMMKKPRCGVPDSGGFM

Pocket interaction

Ca2+

CA pocket interaction

This enzyme binds 3 Ca ions, 2 of them in the catalytic domain.

The residues involved in the Ca996 interactions (coordinate bonds) are .

Zn2+

The zinc-binding motif HEXGHXXGXXH presents in the catalytic domain is characteristic for the protease activity of MMP-8.

Zn999 : the catalytic zinc

It is involved in the catalytic activity. In a publication [6] which studies the catalytic domain of MMP8 thanks to the Pro-Leu-Gly-hydroxylamine inhibitor, this ion is penta-coordinated with: His197, His201 and His207 of MMP8 and with the carbonyl and the hydroxyl oxygen of the hydroxamic acid moiety of the inhibitor. On this you can only see the 3 His of MMP8 with the Zn999. The fourth ligand of the catalytic zinc is a water molecule.

ZN pocket interaction

Zn998 : the structural zinc

This ion is considered as a structural ion. The residues involved in the Zn998 interactions are . The glutamic acid adjacent to the first histidine is essential for catalysis. It's good to know that W Bode and al.[7] were unable to exchange or remove this Zinc in their crystals, which is suggesting that there is a tight interaction with MMP-8.

One of them is as well bound to the Glu residue thanks to a hydrogen bond. The second Zn2+ atom is not involved in the active site. At first, the Gly 206 residue of the substrate binds the active site thanks to the Zn2+ atom. When it binds it takes the place of unstable water molecules and establishes stabilizing interactions with the active site thanks to its C terminal part. Then, the Ala 182 residue of the enzyme makes a hydrogen bond with the NH group of the substrate: this allows the substrate to enter the cavity of the catalytic site. The rest of the protein is stabilized by 4 hydrogen bonds with the amino acid located in the cavity.

The conserved cysteine present in the cysteine-switch motif (89-96) binds the catalytic zinc ion, thus inhibiting the enzyme. The dissociation of the cysteine from the zinc ion upon the activation-peptide release activates the enzyme.

Catalytic domain

This domain is composed of 163 residues, from Met80 to Gly242, organized in and . Thanks to X-ray crystallography, its structure has been solved with 1,7 Å resolution (2OY4). (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC394940/?page=1). The catalytic zinc ion is situated at the bottom of the active-site. The other zinc ion and the two calcium ions are packed against the top of the beta sheet and presumably function to stabilize the catalytic domain. The polypeptide folding and in particular the zinc environment of the collagenase catalytic domain bear a close ressemblance to the astacins and the snake venom metalloproteinases. The catalytic domain alone has proteolytic activity against other protein substrates and synthetic substrates.

Hemopexin domain

The hemopexin domain has two conserved cysteines that are disulfide bonded. Mutation of those cysteines to alanines ^[4] or reduction and alkylation destroys collagenolytic activity (K. Suzuki and H.Nagase, unpublished results).^[3]

[8]

This domain is localized outside of the catalytic domain. It is essential for the substrate recognition of MMP-8 and the single catalytic domain of MMP-8 is not able to cleave collagen. When this hemopexin-like domain is removed, the protein loses its ability to cleave collagen. However, neutrophil collagenase is still able to cleave other substrate. It seems that the collagen binds to two sites on MMP-8 : one in the catalytic site and another in the hemopexin domain. One hypothesis is that when the collagen binds to both sites, its helical structure is destabilized and unwound. Thus, the cleavage site of collagen is accessible and the cleavage reaction can occur.

Mechanism

To express collagenolytic activity, MMP-8 needs to have both the catalytic and hemopexin domains but it is not clear how the hemopexin domain help to cleave triple-helical collagens because it does not bind to collagen.^[5] To allow cleavage of the individual alpha chains of collagen, the binding of collagenases must partially unwind triple helix by inducing a conformational change in alpha chain. However, the molecular basis of this mechanism is not known.^[6] The carbonyl group of the peptide bond coordinates with the active-site zinc. This displaces the water molecule from the zinc atom. The peptide hydrolysis is assisted by the carboxyl group of the glutamate, which serves as a general base to draw a proton from the displaced water molecule, thereby facilitating the nucleophilic attack of the water molecule on the carbonyl carbon of the peptide scissile bond. A pocket to the right of the active-site zinc, called the specificity pocket or , accommodates the side chain of the substrate residue, which becomes the new N-terminus after cleavage. The sizes of the S1′ pocket vary among the MMPs, and this is one of the major determining factors of substrate specificity.

Cleavage at Gly775–Ile776 or Leu776. ^[7]

Function

Like all the MMPs, MMP8 is secreted as inactive proproteins and then activated after a cleavage by extracellular proteinases. Indeed, it can't be activated without removal of the . cleave the helical collagen molecule at a single Gly-Ile/Leu bond in each alpha-chain of the molecule. The cleavage generates fragments that spontaneously lose their helical conformation, denature to gelatin, and become soluble. The gelatin is then susceptible to attack by gelatinases and other proteases^[8] metalloendopeptidase activity = mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.^[9]

Disease

Overexpression of MMP8, or inadequate control by TIMPs, can be associated with a lot of pathological conditions: psoriasis, sclerosis, osteoarthritis, rheumatoid arthritis, osteoporosis, Alzheimer's disease, tumor growh and metastasis.^[10] Neutrophil collagenase or collagenase 2 (MMP-8) is unique among the family of matrix metalloproteinases (MMPs) because of its exclusive pattern of expression in inflammatory conditions.^[11]

Relevance

Structural highlights

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

References

↑ "MMP8 matrix metallopeptidase 8 (neutrophil collagenase)"
↑ Stams T, Spurlino JC, Smith DL, Wahl RC, Ho TF, Qoronfleh MW, Banks TM, Rubin B. Structure of human neutrophil collagenase reveals large S1' specificity pocket. Nat Struct Biol. 1994 Feb;1(2):119-23. PMID:7656015
↑ ^3.0 ^3.1 Substrate specificity of MMPs
↑ Hirose T, Patterson C, Pourmotabbed T, Mainardi CL, Hasty KA. Structure-function relationship of human neutrophil collagenase: identification of regions responsible for substrate specificity and general proteinase activity. Proc Natl Acad Sci U S A. 1993 Apr 1;90(7):2569-73. PMID:8464863
↑ Knauper V, Osthues A, DeClerck YA, Langley KE, Blaser J, Tschesche H. Fragmentation of human polymorphonuclear-leucocyte collagenase. Biochem J. 1993 May 1;291 ( Pt 3):847-54. PMID:8489511
↑ Welgus HG, Jeffrey JJ, Eisen AZ. Human skin fibroblast collagenase. Assessment of activation energy and deuterium isotope effect with collagenous substrates. J Biol Chem. 1981 Sep 25;256(18):9516-21. PMID:6270090
↑ Knauper V, Docherty AJ, Smith B, Tschesche H, Murphy G. Analysis of the contribution of the hinge region of human neutrophil collagenase (HNC, MMP-8) to stability and collagenolytic activity by alanine scanning mutagenesis. FEBS Lett. 1997 Mar 17;405(1):60-4. PMID:9094424
↑ "Neutrophil collagenase"
↑ "Metalloendopeptidase activity"
↑ "Extra Binding Region Induced by Non-Zinc Chelating Inhibitors into the S1′ Subsite of Matrix Metalloproteinase 8"
↑ Balbin M, Fueyo A, Knauper V, Pendas AM, Lopez JM, Jimenez MG, Murphy G, Lopez-Otin C. Collagenase 2 (MMP-8) expression in murine tissue-remodeling processes. Analysis of its potential role in postpartum involution of the uterus. J Biol Chem. 1998 Sep 11;273(37):23959-68. PMID:9727011

RESSOURCE : Image:2oy4 mm1.pdb ( la structure du monomère )

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@@ Line 53: / Line 53: @@
 <scene name='71/719866/Catalytic_site/2'>Catalytic site</scene>
-<scene name='71/719866/S1prime_pocket/1'>S1' pocket</scene>
 === Hemopexin domain ===
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 To express collagenolytic activity, MMP-8 needs to have both the catalytic and hemopexin domains but it is not clear how the hemopexin domain help to cleave triple-helical collagens because it does not bind to collagen.<ref>PMID:8489511</ref>
 To allow cleavage of the individual alpha chains of collagen, the binding of collagenases must partially unwind triple helix by inducing a conformational change in alpha chain. However, the molecular basis of this mechanism is not known.<ref>PMID:6270090</ref>
-The carbonyl group of the peptide bond coordinates with the active-site zinc. This displaces the water molecule from the zinc atom. The peptide hydrolysis is assisted by the carboxyl group of the glutamate, which serves as a general base to draw a proton from the displaced water molecule, thereby facilitating the nucleophilic attack of the water molecule on the carbonyl carbon of the peptide scissile bond. A pocket to the right of the active-site zinc, called the specificity pocket or S1′ pocket, accommodates the side chain of the substrate residue, which becomes the new N-terminus after cleavage. The sizes of the S1′ pocket vary among the MMPs, and this is one of the major determining factors of substrate specificity.
+The carbonyl group of the peptide bond coordinates with the active-site zinc. This displaces the water molecule from the zinc atom. The peptide hydrolysis is assisted by the carboxyl group of the glutamate, which serves as a general base to draw a proton from the displaced water molecule, thereby facilitating the nucleophilic attack of the water molecule on the carbonyl carbon of the peptide scissile bond. A pocket to the right of the active-site zinc, called the specificity pocket or <scene name='71/719866/S1prime_pocket/1'>S1' pocket</scene>, accommodates the side chain of the substrate residue, which becomes the new N-terminus after cleavage. The sizes of the S1′ pocket vary among the MMPs, and this is one of the major determining factors of substrate specificity.