2N8R

Productive complex between MMP-12 and synthetic triple-helical collagen, revealed through paramagnetic NMR


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 7500 
  • Conformers Submitted: 
  • Selection Criteria: back calculated data agree with experimental NOESY spectrum 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Path to Collagenolysis: COLLAGEN V TRIPLE-HELIX MODEL BOUND PRODUCTIVELY AND IN ENCOUNTERS BY MATRIX METALLOPROTEINASE-12.

Prior, S.H.Byrne, T.S.Tokmina-Roszyk, D.Fields, G.B.Van Doren, S.R.

(2016) J.Biol.Chem. 291: 7888-7901

  • DOI: 10.1074/jbc.M115.703124

  • PubMed Abstract: 
  • Collagenolysis is essential in extracellular matrix homeostasis, but its structural basis has long been shrouded in mystery. We have developed a novel docking strategy guided by paramagnetic NMR that positions a triple-helical collagen V mimic (synth ...

    Collagenolysis is essential in extracellular matrix homeostasis, but its structural basis has long been shrouded in mystery. We have developed a novel docking strategy guided by paramagnetic NMR that positions a triple-helical collagen V mimic (synthesized with nitroxide spin labels) in the active site of the catalytic domain of matrix metalloproteinase-12 (MMP-12 or macrophage metalloelastase) primed for catalysis. The collagenolytically productive complex forms by utilizing seven distinct subsites that traverse the entire length of the active site. These subsites bury ∼1,080 Å(2)of surface area, over half of which is contributed by the trailing strand of the synthetic collagen V mimic, which also appears to ligate the catalytic zinc through the glycine carbonyl oxygen of its scissile G∼VV triplet. Notably, the middle strand also occupies the full length of the active site where it contributes extensive interfacial contacts with five subsites. This work identifies, for the first time, the productive and specific interactions of a collagen triple helix with an MMP catalytic site. The results uniquely demonstrate that the active site of the MMPs is wide enough to accommodate two strands from collagen triple helices. Paramagnetic relaxation enhancements also reveal an extensive array of encounter complexes that form over a large part of the catalytic domain. These transient complexes could possibly facilitate the formation of collagenolytically active complexes via directional Brownian tumbling.


    Related Citations: 
    • 1H, 13C, and 15N peak assignments and secondary structure of human macrophage metalloelastase (MMP-12) in its inhibitor-free state.
      Bhaskaran, R.,Van Doren, S.R.
      (2006) J.Biomol.Nmr 36 Suppl 1: 55


    Organizational Affiliation

    From the Department of Biochemistry, University of Missouri, Columbia, Missouri 65211.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage metalloelastase
A
164Homo sapiensMutation(s): 0 
Gene Names: MMP12 (HME)
EC: 3.4.24.65
Find proteins for P39900 (Homo sapiens)
Go to Gene View: MMP12
Go to UniProtKB:  P39900
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Collagen triple helix repeat family protein
B, C, D
36N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
B, C, D
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 7500 
  • Conformers Submitted: 
  • Selection Criteria: back calculated data agree with experimental NOESY spectrum 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-16
    Type: Database references
  • Version 1.2: 2016-04-27
    Type: Database references