4ZLA | pdb_00004zla

Bestatin complex structure of leucine aminopeptidase from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb4ZLA/pdb

• Classification: HYDROLASE/HYDROLASE inhibitor
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-01 Released: 2015-12-23 
• Deposition Author(s): Modak, J.K., Roujeinikova, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.219 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Structural basis for substrate specificity of Helicobacter pylori M17 aminopeptidase.

Modak, J.K., Rut, W., Wijeyewickrema, L.C., Pike, R.N., Drag, M., Roujeinikova, A.

(2016) Biochimie 121: 60-71

• PubMed: 26616008 
• DOI: https://doi.org/10.1016/j.biochi.2015.11.021
• Primary Citation Related Structures: 
  4ZI6, 4ZLA


• PubMed Abstract: 
  

  The M17 aminopeptidase from the carcinogenic gastric bacterium Helicobacter pylori (HpM17AP) is an important housekeeping enzyme involved in catabolism of endogenous and exogenous peptides. It is implicated in H. pylori defence against the human innate immune response and in the mechanism of metronidazole resistance. Bestatin inhibits HpM17AP and suppresses H. pylori growth. To address the structural basis of catalysis and inhibition of this enzyme, we have established its specificity towards the N-terminal amino acid of peptide substrates and determined the crystal structures of HpM17AP and its complex with bestatin. The position of the D-phenylalanine moiety of the inhibitor with respect to the active-site metal ions, bicarbonate ion and with respect to other M17 aminopeptidases suggested that this residue binds to the S1 subsite of HpM17AP. In contrast to most characterized M17 aminopeptidases, HpM17AP displays preference for L-Arg over L-Leu residues in peptide substrates. Compared to very similar homologues from other bacteria, a distinguishing feature of HpM17AP is a hydrophilic pocket at the end of the S1 subsite that is likely to accommodate the charged head group of the L-Arg residue of the substrate. The pocket is flanked by a sodium ion (not present in M17 aminopeptidases that show preference for L-Leu) and its coordinating water molecules. In addition, the structure suggests that variable loops at the entrance to, and in the middle of, the substrate-binding channel are important determinants of substrate specificity of M17 aminopeptidases.

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Organizational Affiliation: 
• Infection and Immunity Program, Monash Biomedical Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia.
Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland.
Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.
Infection and Immunity Program, Monash Biomedical Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 333.99 kDa 
• Atom Count: 25,067 
• Modeled Residue Count: 2,899 
• Deposited Residue Count: 3,012 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosol aminopeptidase	A, B, C, D, E, F	502	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: pepA, HP_0570 EC: 3.4.11.1 (PDB Primary Data), 3.4.11.10 (PDB Primary Data)
UniProt
Find proteins for O25294 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25294  Go to UniProtKB:  O25294

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BES	EA [auth E], JA [auth F], K [auth A], P [auth B], U [auth C], Z [auth D]	2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID C16 H24 N2 O4 VGGGPCQERPFHOB-RDBSUJKOSA-N
ZN	AA [auth E], BA [auth E], FA [auth F], G [auth A], GA [auth F], H [auth A], L [auth B], M [auth B], Q [auth C], R [auth C], V [auth D], W [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
BCT	DA [auth E], IA [auth F], J [auth A], O [auth B], T [auth C], Y [auth D]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
NA	CA [auth E], HA [auth F], I [auth A], N [auth B], S [auth C], X [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.219 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.77	α = 81.89
b = 99.69	β = 60.97
c = 96.78	γ = 75.39

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
Blu-Ice	data collection
PHASER	phasing
MOSFLM	data reduction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-23 
Deposition Author(s): Modak, J.K., Roujeinikova, A.

Revision History  

• Version 1.0: 2015-12-23
  Type: Initial release
  
• Version 1.1: 2016-02-03
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description