2JXY | pdb_00002jxy

Solution structure of the hemopexin-like domain of MMP12


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 1600 
  • Conformers Submitted: 20 
  • Selection Criteria: lowest target function 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Evidence of reciprocal reorientation of the catalytic and hemopexin-like domains of full-length MMP-12

Bertini, I.Calderone, V.Fragai, M.Jaiswal, R.Luchinat, C.Melikian, M.Mylonas, E.Svergun, D.I.

(2008) J Am Chem Soc 130: 7011-7021

  • DOI: https://doi.org/10.1021/ja710491y
  • Primary Citation Related Structures: 
    2JXY, 3BA0

  • PubMed Abstract: 

    The proteolytic activity of matrix metalloproteinases toward extracellular matrix components (ECM), cytokines, chemokines, and membrane receptors is crucial for several homeostatic and pathological processes. Active MMPs are a family of single-chain enzymes (23 family members in the human genome), most of which constituted by a catalytic domain and by a hemopexin-like domain connected by a linker. The X-ray structures of MMP-1 and MMP-2 suggest a conserved and well-defined spatial relationship between the two domains. Here we present structural data for MMP-12, suitably stabilized against self-hydrolysis, both in solution (NMR and SAXS) and in the solid state (X-ray), showing that the hemopexin-like and the catalytic domains experience conformational freedom with respect to each other on a time scale shorter than 10(-8) s. Hints on the probable conformations are also obtained. This experimental finding opens new perspectives for the often hypothesized active role of the hemopexin-like domain in the enzymatic activity of MMPs.


  • Organizational Affiliation
    • Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. ivanobertini@cerm.unifi.it

Macromolecule Content 

  • Total Structure Weight: 23.24 kDa 
  • Atom Count: 1,648 
  • Modeled Residue Count: 194 
  • Deposited Residue Count: 194 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Macrophage metalloelastase194Homo sapiensMutation(s): 0 
EC: 3.4.24.65
UniProt & NIH Common Fund Data Resources
Find proteins for P39900 (Homo sapiens)
Explore P39900 
Go to UniProtKB:  P39900
PHAROS:  P39900
GTEx:  ENSG00000262406 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39900
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1600 
  • Conformers Submitted: 20 
  • Selection Criteria: lowest target function 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-16
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-11-13
    Changes: Data collection, Structure summary