5ZJK

Structure of myroilysin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of mature myroilysin and implication for its activation mechanism.

Ran, T.Li, W.Sun, B.Xu, M.Qiu, S.Xu, D.Q.He, J.Wang, W.

(2019) Int J Biol Macromol 

  • DOI: https://doi.org/10.1016/j.ijbiomac.2019.11.205
  • Primary Citation of Related Structures:  
    5ZJK

  • PubMed Abstract: 

    Myroilysin is a novel bacterial member of M12A metalloproteases family with an uncommon "cysteine switch" activation mechanism and a unique "cap" structure. However, activation of pro-myroilysin is elusive. Here, mature myroilysin was obtained for structure determination by treating pro-myroilysin with trypsin. The structure of mature myroilysin showed that the active-site zinc ion of the mature protein is coordinated by three histidine residues, a water molecule, and a tyrosine residue (Tyr208) in the conserved Met-turn motif (SIMHY). The "cap" structure moves away from the active-site to leave the active cleft open; the newly formed N-terminus is deeply buried in myroilysin, and Glu151 forms a salt bridge directly with the first amino acid residue (Gly38), whereas they are far from each other in the pro-myroilysin. The mutation of Tyr208 indicates that Tyr208 plays an important role in activity of myroilysin. The proteolytic activity and thermostability of mutant E151A decreased dramatically, implying that Glu151 is not only important for catalysis, but also crucial for structural stability in myroilysin. Structural comparison also reveals differences existed between myroilysin and astacin. Our biochemical and structural data provide new insights into the activation of myroilysin and functional involvement of crucial residues Tyr208 and Glu151.


  • Organizational Affiliation

    Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myroilysin
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
213Myroides sp. CSLB8Mutation(s): 0 
UniProt
Find proteins for A0A0P0DZ84 (Myroides sp. CSLB8)
Explore A0A0P0DZ84 
Go to UniProtKB:  A0A0P0DZ84
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0P0DZ84
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth F]
CA [auth G]
EA [auth H]
GA [auth I]
IA [auth J]
AA [auth F],
CA [auth G],
EA [auth H],
GA [auth I],
IA [auth J],
KA [auth K],
NA [auth M],
RA [auth P],
T [auth B],
TA [auth Q],
W [auth D],
Y [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth F]
DA [auth G]
FA [auth H]
HA [auth I]
JA [auth J]
BA [auth F],
DA [auth G],
FA [auth H],
HA [auth I],
JA [auth J],
LA [auth K],
MA [auth L],
OA [auth M],
PA [auth N],
QA [auth O],
S [auth A],
SA [auth P],
U [auth B],
UA [auth Q],
V [auth C],
VA [auth R],
X [auth D],
Z [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.176α = 90
b = 115.902β = 93.71
c = 163.354γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31770074
National Natural Science Foundation of ChinaChina31770050

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2020-06-03
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Derived calculations