5ZJK | pdb_00005zjk

Structure of myroilysin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.254 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5ZJK

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 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.

Macromolecule Content 

  • Total Structure Weight: 435.82 kDa 
  • Atom Count: 30,072 
  • Modeled Residue Count: 3,683 
  • Deposited Residue Count: 3,834 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
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