4WVP

Crystal structure of an activity-based probe HNE complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The Elastase-PK101 Structure: Mechanism of an Ultrasensitive Activity-based Probe Revealed.

Lechtenberg, B.C.Kasperkiewicz, P.Robinson, H.Drag, M.Riedl, S.J.

(2015) Acs Chem.Biol. 10: 945-951

  • DOI: 10.1021/cb500909n

  • PubMed Abstract: 
  • Human neutrophil elastase (HNE) plays a central role in neutrophil host defense, but its broad specificity makes HNE a difficult target for both inhibitor and probe development. Recently, we identified the unnatural amino acid containing activity-bas ...

    Human neutrophil elastase (HNE) plays a central role in neutrophil host defense, but its broad specificity makes HNE a difficult target for both inhibitor and probe development. Recently, we identified the unnatural amino acid containing activity-based probe PK101, which exhibits astounding sensitivity and selectivity for HNE, yet completely lacks mechanistic explanation for its unique characteristics. Here, we present the crystal structure of the HNE-PK101 complex which not only reveals the basis for PK101 ultrasensitivity but also uncovers so far unrecognized HNE features. Strikingly, the Nle(O-Bzl) function in the P4 position of PK101 reveals and leverages an "exo-pocket" on HNE as a critical factor for selectivity. Furthermore, the PK101 P3 position harbors a methionine dioxide function, which mimics a post-translationally oxidized methionine residue and forms a critical hydrogen bond to the backbone amide of Gly219 of HNE. Gly219 resides in a Gly-Gly motif that is unique to HNE, yet compulsory for this interaction. Consequently, this feature enables HNE to accommodate substrates that have undergone methionine oxidation, which constitutes a hallmark post-translational modification of neutrophil signaling.


    Organizational Affiliation

    †Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neutrophil elastase
E
218Homo sapiensMutation(s): 0 
Gene Names: ELANE (ELA2)
EC: 3.4.21.37
Find proteins for P08246 (Homo sapiens)
Go to Gene View: ELANE
Go to UniProtKB:  P08246
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BTN-3V3-NLB-OMT-OIC-3V2
I
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
E, I
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
E
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
E
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002139
Query on PRD_002139
I6-mer peptide BTN-PE5-NLB-OMT-OIC-AXYPeptide-like / Inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.138 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 73.120α = 90.00
b = 73.120β = 90.00
c = 69.451γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
MOSFLMdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-04-08
    Type: Advisory
  • Version 1.2: 2015-04-29
    Type: Database references
  • Version 1.3: 2015-09-09
    Type: Refinement description
  • Version 1.4: 2017-11-22
    Type: Derived calculations, Refinement description