5GWD

Structure of Myroilysin

  • Classification: HYDROLASE
  • Organism(s): Myroides sp. CSLB8
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2016-09-10 Released: 2017-02-15 
  • Deposition Author(s): Xu, D., Ran, T., Wang, W.
  • Funding Organization(s): National Natural Science Foundation of China, the Natural Science Foundation of Jiangsu Province

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Myroilysin Is a New Bacterial Member of the M12A Family of Metzincin Metallopeptidases and Is Activated by a Cysteine Switch Mechanism.

Xu, D.Zhou, J.Lou, X.He, J.Ran, T.Wang, W.

(2017) J Biol Chem 292: 5195-5206

  • DOI: 10.1074/jbc.M116.758110
  • Primary Citation of Related Structures:  
    5CZW, 5GWD

  • PubMed Abstract: 
  • Proteases play important roles in all living organisms and also have important industrial applications. Family M12A metalloproteases, mainly found throughout the animal kingdom, belong to the metzincin protease family and are synthesized as inactive precursors ...

    Proteases play important roles in all living organisms and also have important industrial applications. Family M12A metalloproteases, mainly found throughout the animal kingdom, belong to the metzincin protease family and are synthesized as inactive precursors. So far, only flavastacin and myroilysin, isolated from bacteria, were reported to be M12A proteases, whereas the classification of myroilysin is still unclear due to the lack of structural information. Here, we report the crystal structures of pro-myroilysin from bacterium Myroides sp. cslb8. The catalytic zinc ion of pro-myroilysin, at the bottom of a deep active site, is coordinated by three histidine residues in the conserved motif HE XX H XX G XX H; the cysteine residue in the pro-peptide coordinates the catalytic zinc ion and inhibits myroilysin activity. Structure comparisons revealed that myroilysin shares high similarity with the members of the M12A, M10A, and M10B families of metalloproteases. However, a unique "cap" structure tops the active site cleft in the structure of pro-myroilysin, and this "cap" structure does not exist in the above structure-reported subfamilies. Further structure-based sequence analysis revealed that myroilysin appears to belong to the M12A family, but pro-myroilysin uses a "cysteine switch" activation mechanism with a unique segment, including the conserved cysteine residue, whereas other reported M12A family proteases use an "aspartate switch" activation mechanism. Thus, our results suggest that myroilysin is a new bacterial member of the M12A family with an exceptional cysteine switch activation mechanism. Our results shed new light on the classification of the M12A family and may suggest a divergent evolution of the M12 family.


    Organizational Affiliation

    From the Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China and wwwang@njau.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MyroilysinA, B252Myroides sp. CSLB8Mutation(s): 0 
UniProt
Find proteins for A0A0P0DZ84 (Myroides sp. CSLB8)
Explore A0A0P0DZ84 
Go to UniProtKB:  A0A0P0DZ84
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
A, BL-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.223α = 90
b = 35.486β = 101.41
c = 93.757γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
SHELXCDphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-09-10 
  • Released Date: 2017-02-15 
  • Deposition Author(s): Xu, D., Ran, T., Wang, W.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31170686
National Natural Science Foundation of ChinaChina31100028
National Natural Science Foundation of ChinaChina31400055
the Natural Science Foundation of Jiangsu ProvinceChinaBK20140690

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-02-22
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Data collection, Database references
  • Version 1.3: 2017-10-18
    Changes: Author supporting evidence