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Orientation in Solution of MMP-3 Catalytic Domain and N-TIMP-1 from Residual Dipolar Couplings


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 25 
  • Conformers Submitted: 
  • Selection Criteria: lowest energy structure 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Global Orientation of Bound MMP-3 and N-TIMP-1 in Solution via Residual Dipolar Couplings

Arumugam, S.Van Doren, S.R.

(2003) Biochemistry 42: 7950-7958

  • DOI: 10.1021/bi034545s

  • PubMed Abstract: 
  • Crystal structures of catalytic domains of MMP-3 and MT1-MMP bound to TIMP-1 or TIMP-2, respectively, differ in the orientation of the TIMP in the MMP active site. The orientation in solution of N-TIMP-1 in the MMP-3 active site has been investigated ...

    Crystal structures of catalytic domains of MMP-3 and MT1-MMP bound to TIMP-1 or TIMP-2, respectively, differ in the orientation of the TIMP in the MMP active site. The orientation in solution of N-TIMP-1 in the MMP-3 active site has been investigated using residual dipolar couplings (RDCs). Fitting of the RDCs to the X-ray structures of the complexes suggests general agreement with the orientation of crystalline MMP-3(DeltaC) and TIMP-1 and a large disparity from the orientation of crystalline MT1-MMP(DeltaC) and TIMP-2. Rigid body docking of MMP-3 and N-TIMP-1 X-ray coordinates using RDCs and intermolecular NOEs provided a time-averaged orientation in solution differing from the crystal structure by a 5 degrees rotation toward the MT1-MMP(DeltaC)/TIMP-2 orientation. The slight discrepancy in orientations in solution and crystal lies within the experimental uncertainties. Intermolecular NOEs used in the docking corroborated the accuracy of mapping the interface by a paramagnetic NMR footprinting assay, a potential alternative source of contacts for docking. Some uncertainty in the N-TIMP-1 orientation in the MMP-3 active site, coupled with microsecond to millisecond fluctuations of the MMP-binding ridge of N-TIMP-1 in the complex and flexibility in MMP-3(DeltaC) S(1)' to S(3)' subsites, leaves open the possibility that N-TIMP-1 might dynamically pivot a few degrees or more in the arc toward the MT1-MMP(DeltaC)/TIMP-2 orientation. Differing TIMP orientations in MMP active sites are more likely to result from structural differences in TIMP AB hairpin loops than from crystal packing artifacts.


    Organizational Affiliation

    Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, Missouri 65211, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Stromelysin-1
A
168Homo sapiensMutation(s): 0 
Gene Names: MMP3 (STMY1)
EC: 3.4.24.17
Find proteins for P08254 (Homo sapiens)
Go to Gene View: MMP3
Go to UniProtKB:  P08254
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Metalloproteinase inhibitor 1
B
126Homo sapiensMutation(s): 0 
Gene Names: TIMP1 (CLGI, TIMP)
Find proteins for P01033 (Homo sapiens)
Go to Gene View: TIMP1
Go to UniProtKB:  P01033
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 25 
  • Conformers Submitted: 
  • Selection Criteria: lowest energy structure 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-29
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance