PDBsum entry 4g0d

Hydrolase

PDB id: 4g0d

Contents

Protein chains

368 a.a.

19 a.a.

26 a.a.

23 a.a.

Ligands

PGO ×38

PEG ×4

GOL ×5

Metals

_CL ×8

_ZN ×8

_CA ×23

Waters ×896

PDB id:

4g0d

Name:

Hydrolase

Title:

Human collagenase 3 (mmp-13) full form with peptides from pro-domain

Structure:

Collagenase 3. Chain: a, b, c, d. Fragment: inactive full form (unp residues 104-471). Synonym: matrix metalloproteinase-13, mmp-13. Engineered: yes. Mutation: yes. Collagenase 3, pro-domain peptide. Chain: w, x, y, z. Fragment: pro-domain fragment (unp residues 25-50).

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: mmp13. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.54Å R-factor: 0.172 R-free: 0.241

Authors:

E.A.Stura,L.Vera,R.Visse,H.Nagase,V.Dive

Key ref:

E.A.Stura et al. (2013). Crystal structure of full-length human collagenase 3 (MMP-13) with peptides in the active site defines exosites in the catalytic domain. Faseb J, 27, 4395-4405. PubMed id: 23913860 DOI: 10.1096/fj.13-233601

Date:

09-Jul-12 Release date: 21-Aug-13

Protein chains

P45452  (MMP13_HUMAN) -  Collagenase 3 from Homo sapiens

Seq: 471 a.a.

Struc: 368 a.a.*

Protein chain

P45452  (MMP13_HUMAN) -  Collagenase 3 from Homo sapiens

Seq: 471 a.a.

Struc: 19 a.a.

Protein chain

P45452  (MMP13_HUMAN) -  Collagenase 3 from Homo sapiens

Seq: 471 a.a.

Struc: 26 a.a.

Protein chains

P45452  (MMP13_HUMAN) -  Collagenase 3 from Homo sapiens

Seq: 471 a.a.

Struc: 23 a.a.

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

Enzyme reactions

• Enzyme class: Chains A, B, C, D, W, X, Y, Z: E.C.3.4.24.- - ?????

DOI no: 10.1096/fj.13-233601

Faseb J 27:4395-4405 (2013)

PubMed id: 23913860

Crystal structure of full-length human collagenase 3 (MMP-13) with peptides in the active site defines exosites in the catalytic domain.

E.A.Stura, R.Visse, P.Cuniasse, V.Dive, H.Nagase.

ABSTRACT

Matrix metalloproteinase (MMP)-13 is one of the mammalian collagenases that play key roles in tissue remodelling and repair and in progression of diseases such as cancer, arthritis, atherosclerosis, and aneurysm. For collagenase to cleave triple helical collagens, the triple helical structure has to be locally unwound before hydrolysis, but this process is not well understood. We report crystal structures of catalytically inactive full-length human MMP-13(E223A) in complex with peptides of 14-26 aa derived from the cleaved prodomain during activation. Peptides are bound to the active site of the enzyme by forming an extended β-strand with Glu(40) or Tyr(46) inserted into the S1' specificity pocket. The structure of the N-terminal part of the peptides is variable and interacts with different parts of the catalytic domain. Those areas are designated substrate-dependent exosites, in that they accommodate different peptide structures, whereas the precise positioning of the substrate backbone is maintained in the active site. These modes of peptide-MMP-13 interactions have led us to propose how triple helical collagen strands fit into the active site cleft of the collagenase.-Stura, E. A., Visse, R., Cuniasse, P., Dive, V., Nagase, H. Crystal structure of full-length human collagenase 3 (MMP-13) with peptides in the active site defines exosites in the catalytic domain.