Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.03 kDa 
• Atom Count: 1660 
• Residue Count: 176 
• Unique protein chains: 2

3AYU

Crystal structure of MMP-2 active site mutant in complex with APP-drived decapeptide inhibitor

• DOI: 10.2210/pdb3AYU/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-05-17 Released: 2011-08-03 
• Deposition Author(s): Hashimoto, H., Takeuchi, T., Komatsu, K., Miyazaki, K., Sato, M., Higashi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.205 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Literature

Structural basis for matrix metalloproteinase-2 (MMP-2)-selective inhibitory action of {beta}-amyloid precursor protein-derived inhibitor

Hashimoto, H., Takeuchi, T., Komatsu, K., Miyazaki, K., Sato, M., Higashi, S.

(2011) J Biol Chem 

• PubMed: 21813640 
• DOI: 10.1074/jbc.M111.264176
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Unlike other synthetic or physiological inhibitors for matrix metalloproteinases (MMPs), the β-amyloid precursor protein-derived inhibitory peptide (APP-IP) having an ISYGNDALMP sequence has a high selectivity toward MMP-2. Our previous study identified amino acid residues of MMP-2 essential for its selective inhibition by APP-IP and demonstrated that the N to C direction of the decapeptide inhibitor relative to the substrate-binding cleft of MMP-2 is opposite that of substrate. However, detailed interactions between the two molecules remained to be clarified. Here, we determined the crystal structure of the catalytic domain of MMP-2 in complex with APP-IP. We found that APP-IP in the complex is indeed embedded into the substrate-binding cleft of the catalytic domain in the N to C direction opposite that of substrate. With the crystal structure, it was first clarified that the aromatic side chain of Tyr(3) of the inhibitor is accommodated into the S1' pocket of the protease, and the carboxylate group of Asp(6) of APP-IP coordinates bidentately to the catalytic zinc of the enzyme. The Ala(7) to Pro(10) and Tyr(3) to Ile(1) strands of the inhibitor extend into the nonprime and the prime sides of the cleft, respectively. Therefore, the decapeptide inhibitor has long range contact with the substrate-binding cleft of the protease. This mode of interaction is probably essential for the high MMP-2 selectivity of the inhibitor because MMPs share a common architecture in the vicinity of the catalytic center, but whole structures of their substrate-binding clefts have sufficient variety for the inhibitor to distinguish MMP-2 from other MMPs.

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Organizational Affiliation: 

Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
72 kDa type IV collagenase	A	167	Homo sapiens	Mutation(s): 3  Gene Names: MMP2, CLG4A EC: 3.4.24.24
Find proteins for P08253 (Homo sapiens) Explore P08253  Go to UniProtKB:  P08253
NIH Common Fund Data Resources
PHAROS  P08253 GTEx  ENSG00000087245

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Amyloid beta A4 protein	B	10	Homo sapiens	Mutation(s): 0  Gene Names: APP, A4, AD1
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
NIH Common Fund Data Resources
PHAROS  P05067

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.205 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.881	α = 90
b = 76.06	β = 90
c = 37.082	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-17 
• Released Date: 2011-08-03 
Deposition Author(s): Hashimoto, H., Takeuchi, T., Komatsu, K., Miyazaki, K., Sato, M., Higashi, S.

Revision History 

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2011-08-10
  Changes: Structure summary
• Version 1.2: 2011-08-17
  Changes: Database references
• Version 1.3: 2017-08-09
  Changes: Source and taxonomy