5JBT

Mesotrypsin in complex with cleaved amyloid precursor like protein 2 inhibitor (APLP2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis.

Kayode, O.Wang, R.Pendlebury, D.F.Cohen, I.Henin, R.D.Hockla, A.Soares, A.S.Papo, N.Caulfield, T.R.Radisky, E.S.

(2016) J. Biol. Chem. 291: 26304-26319

  • DOI: 10.1074/jbc.M116.758417

  • PubMed Abstract: 
  • The molecular basis of enzyme catalytic power and specificity derives from dynamic interactions between enzyme and substrate during catalysis. Although considerable effort has been devoted to understanding how conformational dynamics within enzymes a ...

    The molecular basis of enzyme catalytic power and specificity derives from dynamic interactions between enzyme and substrate during catalysis. Although considerable effort has been devoted to understanding how conformational dynamics within enzymes affect catalysis, the role of conformational dynamics within protein substrates has not been addressed. Here, we examine the importance of substrate dynamics in the cleavage of Kunitz-bovine pancreatic trypsin inhibitor protease inhibitors by mesotrypsin, finding that the varied conformational dynamics of structurally similar substrates can profoundly impact the rate of catalysis. A 1.4-Å crystal structure of a mesotrypsin-product complex formed with a rapidly cleaved substrate reveals a dramatic conformational change in the substrate upon proteolysis. By using long all-atom molecular dynamics simulations of acyl-enzyme intermediates with proteolysis rates spanning 3 orders of magnitude, we identify global and local dynamic features of substrates on the nanosecond-microsecond time scale that correlate with enzymatic rates and explain differential susceptibility to proteolysis. By integrating multiple enhanced sampling methods for molecular dynamics, we model a viable conformational pathway between substrate-like and product-like states, linking substrate dynamics on the nanosecond-microsecond time scale with large collective substrate motions on the much slower time scale of catalysis. Our findings implicate substrate flexibility as a critical determinant of catalysis.


    Organizational Affiliation

    From the Departments of Cancer Biology and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PRSS3 protein
A
224Homo sapiensMutation(s): 1 
Gene Names: PRSS3 (PRSS4, TRY3, TRY4)
EC: 3.4.21.4
Find proteins for P35030 (Homo sapiens)
Go to Gene View: PRSS3
Go to UniProtKB:  P35030
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Amyloid-like protein 2
X
14Homo sapiensMutation(s): 0 
Gene Names: APLP2 (APPL2)
Find proteins for Q06481 (Homo sapiens)
Go to Gene View: APLP2
Go to UniProtKB:  Q06481
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Amyloid-like protein 2
Y
38Homo sapiensMutation(s): 0 
Gene Names: APLP2 (APPL2)
Find proteins for Q06481 (Homo sapiens)
Go to Gene View: APLP2
Go to UniProtKB:  Q06481
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
Y
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.956α = 90.00
b = 54.539β = 90.00
c = 56.632γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesR01CA154387

Revision History 

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-11-16
    Type: Refinement description
  • Version 1.2: 2016-12-28
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence