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

Experimental Data Snapshot

  • Resolution: 1.76 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1111/mmi.12412
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deseasin MCP-01
A, B
334Pseudoalteromonas sp. SM9913Mutation(s): 0 
Gene Names: PSM_B0251
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.76 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.792α = 90
b = 72.454β = 90
c = 137.627γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Data collection
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description