4DGJ | pdb_00004dgj

Structure of a human enteropeptidase light chain variant

• PDB DOI: https://doi.org/10.2210/pdb4DGJ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-01-26 Released: 2012-04-18 
• Deposition Author(s): Zahn, M., Simeonov, P., Straeter, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Crystal structure of a supercharged variant of the human enteropeptidase light chain.

Simeonov, P., Zahn, M., Strater, N., Zuchner, T.

(2012) Proteins 80: 1907-1910

• PubMed: 22488687 
• DOI: https://doi.org/10.1002/prot.24084
• Primary Citation Related Structures: 
  4DGJ


• PubMed Abstract: 
  

  The highly specific serine protease human enteropeptidase light chain cleaves the Asp4Lys recognition sequence and represents an interesting enzyme for biotechnological applications. The human enzyme shows 10 times faster kinetics compared to other animal sources but low solubility under low salt conditions, which hampers protein production and crystallization. Therefore, a supercharged variant (N6D/G21D/G22D/N142D/K210E/C112S) with increased solubility was used for crystallization. The structure (resolution, 1.9 Å) displays a typical α/β trypsin-like serine protease-fold. The mutations introduced for protein supercharging generate larger clusters of negative potential on both sites of the active cleft but do not affect the structural integrity of the protein.

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Organizational Affiliation: 
• Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 105.52 kDa 
• Atom Count: 8,393 
• Modeled Residue Count: 938 
• Deposited Residue Count: 940 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enteropeptidase catalytic light chain	A, B, C, D	235	Homo sapiens	Mutation(s): 6  Gene Names: TMPRSS15, ENTK, PRSS7 EC: 3.4.21.9
UniProt & NIH Common Fund Data Resources
Find proteins for P98073 (Homo sapiens) Explore P98073  Go to UniProtKB:  P98073
PHAROS:  P98073 GTEx:  ENSG00000154646

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.181	α = 90
b = 147.704	β = 90
c = 148.654	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-18 
Deposition Author(s): Zahn, M., Simeonov, P., Straeter, N.

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2012-04-25
  Changes: Database references
• Version 1.2: 2012-06-20
  Changes: Database references
• Version 1.3: 2020-10-21
  Changes: Data collection, Database references
• Version 1.4: 2024-11-27
  Changes: Data collection, Database references, Structure summary