5L44

Structure of K-26-DCP in complex with the K-26 tripeptide

• PDB DOI: https://doi.org/10.2210/pdb5L44/pdb

• Classification: HYDROLASE
• Organism(s): Astrosporangium hypotensionis K-26
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-24 Released: 2016-10-26 
• Deposition Author(s): Masuyer, G., Acharya, K.R., Kramer, G.J., Bachmann, B.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.213 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Crystal structure of a peptidyl-dipeptidase K-26-DCP from Actinomycete in complex with its natural inhibitor.

Masuyer, G., Cozier, G.E., Kramer, G.J., Bachmann, B.O., Acharya, K.R.

(2016) FEBS J 283: 4357-4369

• PubMed: 27754586 
• DOI: https://doi.org/10.1111/febs.13928
• Primary Citation of Related Structures:  
  5L43, 5L44


• PubMed Abstract: 
  

  Several soil-derived Actinobacteria produce secondary metabolites that are proven specific and potent inhibitors of the human angiotensin-I-converting enzyme (ACE), a key target for the modulation of hypertension through its role in the renin-angiotensin-aldosterone system. K-26-DCP is a zinc dipeptidyl carboxypeptidase (DCP) produced by Astrosporangium hypotensionis, and an ancestral homologue of ACE. Here we report the high-resolution crystal structures of K-26-DCP and of its complex with the natural microbial tripeptide product K-26. The experimental results provide the structural basis for better understanding the specificity of K-26 for human ACE over bacterial DCPs.

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Organizational Affiliation: 

Department of Biology and Biochemistry, University of Bath, UK.

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)

Macromolecule Content

• Total Structure Weight: 154.68 kDa 
• Atom Count: 11,677 
• Modelled Residue Count: 1,324 
• Deposited Residue Count: 1,366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
K-26 dipeptidyl carboxypeptidase	A, B	683	Astrosporangium hypotensionis K-26	Mutation(s): 0
UniProt
Find proteins for A0A1L1QK30 (Astrosporangium hypotensionis K-26) Explore A0A1L1QK30  Go to UniProtKB:  A0A1L1QK30

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K26	G [auth A], L [auth B]	N-ACETYL-L-ILE-L-TYR-(R)-1-AMINO-2-(4-HYDROXYPHENYL)ETHYLPHOSPHONIC ACID C25 H34 N3 O8 P ZFRNBYWFOLDQKG-FDMHNHSTSA-N
SO4	F [auth A], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], E [auth A], I [auth B], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.213 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.58	α = 97.72
b = 66.94	β = 90.71
c = 102	γ = 117.37

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Masuyer, G., Acharya, K.R., Kramer, G.J., Bachmann, B.O.

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2016-11-02
  Changes: Database references
• Version 1.2: 2016-12-14
  Changes: Database references
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description