3VV3

Crystal structure of deseasin MCP-01 from Pseudoalteromonas sp. SM9913


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and mechanistic insights into collagen degradation by a bacterial collagenolytic serine protease in the subtilisin family.

Ran, L.Y.Su, H.N.Zhao, G.Y.Gao, X.Zhou, M.Y.Wang, P.Zhao, H.L.Xie, B.B.Zhang, X.Y.Chen, X.L.Zhou, B.C.Zhang, Y.Z.

(2013) Mol. Microbiol. 90: 997-1010

  • DOI: 10.1111/mmi.12412

  • PubMed Abstract: 
  • A number of proteases in the subtilisin family derived from environmental or pathogenic microorganisms have been reported to be collagenolytic serine proteases. However, their collagen degradation mechanisms remain unclear. Here, the degradation mech ...

    A number of proteases in the subtilisin family derived from environmental or pathogenic microorganisms have been reported to be collagenolytic serine proteases. However, their collagen degradation mechanisms remain unclear. Here, the degradation mechanism of type I collagen fibres by the S8 collagenolytic protease MCP-01, from Pseudoalteromonas sp. SM9913, was studied. Atomic force microscopy observation and biochemical analysis confirmed that MCP-01 progressively released single fibrils from collagen fibres and released collagen monomers from fibrils mainly by hydrolysing proteoglycans and telopeptides in the collagen fibres. Structural and mutational analyses indicated that an enlarged substrate-binding pocket, mainly composed of loops 7, 9 and 11, is necessary for collagen recognition and that the acidic and aromatic residues on these loops form a negatively charged, hydrophobic environment for collagen binding. MCP-01 displayed a non-strict preference for peptide bonds with Pro or basic residues at the P1 site and/or Gly at the P1' site in collagen. His211 is a key residue for the P1-basic-residue preference of MCP-01. Our study gives structural and mechanistic insights into collagen degradation of the S8 collagenolytic protease, which is helpful in developing therapeutics for diseases with S8 collagenolytic proteases as pathogenic factors and in studying environmental organic nitrogen degradation mechanisms.


    Organizational Affiliation

    State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China; Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deseasin MCP-01
A, B
334N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.792α = 90.00
b = 72.454β = 90.00
c = 137.627γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Data collection, Database references
  • Version 1.2: 2019-12-04
    Type: Data collection