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 
  • R-Value Observed: 0.140 

wwPDB Validation 3D Report Full Report



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
  • Primary Citation of Related Structures:  
    4WVP

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Neutrophil elastaseE218Homo sapiensMutation(s): 0 
Gene Names: ELANEELA2
EC: 3.4.21.37
Find proteins for P08246 (Homo sapiens)
Explore P08246 
Go to UniProtKB:  P08246
NIH Common Fund Data Resources
PHAROS  P08246
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BTN-3V3-NLB-OMT-OIC-3V2I6synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
A
4 N-Glycosylation
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
B
3 N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download CCD File 
E
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NLB
Query on NLB
IL-PEPTIDE LINKINGC13 H19 N O3LEU
OMT
Query on OMT
IL-PEPTIDE LINKINGC5 H11 N O4 SMET
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002139
Query on PRD_002139
I6-mer peptide BTN-PE5-NLB-OMT-OIC-AXYPeptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.12α = 90
b = 73.12β = 90
c = 69.451γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-04-08
    Changes: Advisory
  • Version 1.2: 2015-04-29
    Changes: Database references
  • Version 1.3: 2015-09-09
    Changes: Refinement description
  • Version 1.4: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary