9G5J | pdb_00009g5j

Structure of the PRO-PRO endopeptidase (PPEP-3) E153A Y189F in complex with substrate peptide Ac-EPLPPPP-NH2 from Geobacillus thermodenitrificans

• PDB DOI: https://doi.org/10.2210/pdb9G5J/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus thermodenitrificans NG80-2, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-07-17 Released: 2025-07-30 
• Deposition Author(s): Claushuis, B., Wojtalla, F., van Leeuwen, H., Corver, J., Baumann, U., Hensbergen, P.
• Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Structural analyses and substrate profiling of PPEP-3 provide new insights into the molecular basis of Pro-Pro endopeptidase specificity

Claushuis, B., Wojtalla, F., Papenhagen, L., Cordfunke, R.A., de Ru, A.H., van Leeuwen, H.C., Corver, J., Hensbergen, P.J., Baumann, U.

(2026) iScience 29: 114360

• DOI: https://doi.org/10.1016/j.isci.2025.114360

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 108.92 kDa 
• Atom Count: 7,485 
• Modeled Residue Count: 871 
• Deposited Residue Count: 956 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATLF-like domain-containing protein	A, B, C, D	230	Geobacillus thermodenitrificans NG80-2	Mutation(s): 2  Gene Names: GTNG_1672
UniProt
Find proteins for A4INY2 (Geobacillus thermodenitrificans (strain NG80-2)) Explore A4INY2  Go to UniProtKB:  A4INY2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-GLU-PRO-LEU-PRO-PRO-PRO-PRO-NH2	E, F, G, H	9	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	J [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	N [auth D]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	I [auth A], K [auth B], L [auth C], M [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.43	α = 90
b = 95.41	β = 90
c = 126.81	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Claushuis, B., Wojtalla, F., van Leeuwen, H., Corver, J., Baumann, U., Hensbergen, P.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	OCENW.KLEIN.103

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release
  
• Version 1.1: 2026-02-04
  Changes: Data collection, Database references