1OO9

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 

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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
  • Primary Citation of Related Structures:  
    1OO9

  • 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 using residual dipolar couplings (RDCs) ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Stromelysin-1A168Homo sapiensMutation(s): 0 
Gene Names: MMP3 OR STMY1MMP3STMY1
EC: 3.4.24.17
UniProt & NIH Common Fund Data Resources
Find proteins for P08254 (Homo sapiens)
Explore P08254 
Go to UniProtKB:  P08254
PHAROS:  P08254
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Metalloproteinase inhibitor 1B126Homo sapiensMutation(s): 0 
Gene Names: TIMP1 OR TIMP OR CLGITIMP1CLGITIMP
UniProt & NIH Common Fund Data Resources
Find proteins for P01033 (Homo sapiens)
Explore P01033 
Go to UniProtKB:  P01033
PHAROS:  P01033
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 25 
  • Conformers Submitted: 
  • Selection Criteria: lowest energy structure 
  • OLDERADO: 1OO9 Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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