1FY2 | pdb_00001fy2

Aspartyl Dipeptidase

• PDB DOI: https://doi.org/10.2210/pdb1FY2/pdb

• Classification: HYDROLASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-09-28 Released: 2001-01-10 
• Deposition Author(s): Hakansson, K., Wang, A.H.-J., Miller, C.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.230 (Depositor) 
• R-Value Work: 
  0.218 (Depositor), 0.216 (DCC) 

Literature

The structure of aspartyl dipeptidase reveals a unique fold with a Ser-His-Glu catalytic triad.

Hakansson, K., Wang, A.H., Miller, C.G.

(2000) Proc Natl Acad Sci U S A 97: 14097-14102

• PubMed: 11106384 
• DOI: https://doi.org/10.1073/pnas.260376797
• Primary Citation Related Structures: 
  1FY2, 1FYE


• PubMed Abstract: 
  

  The three-dimensional structure of Salmonella typhimurium aspartyl dipeptidase, peptidase E, was solved crystallographically and refined to 1.2-A resolution. The structure of this 25-kDa enzyme consists of two mixed beta-sheets forming a V, flanked by six alpha-helices. The active site contains a Ser-His-Glu catalytic triad and is the first example of a serine peptidase/protease with a glutamate in the catalytic triad. The active site Ser is located on a strand-helix motif reminiscent of that found in alpha/beta-hydrolases, but the polypeptide fold and the organization of the catalytic triad differ from those of the known serine proteases. This enzyme is a member of a family of serine hydrolases and appears to represent a new example of convergent evolution of peptidase activity.

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Organizational Affiliation: 
• Departments of Microbiology and Cell and Structural Biology, B103 Chemical and Life Science Laboratory, University of Illinois at Urbana-Champaign, 601 South Goodwin Avenue, Urbana, IL 61801, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.91 kDa 
• Atom Count: 1,877 
• Modeled Residue Count: 220 
• Deposited Residue Count: 229 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ASPARTYL DIPEPTIDASE	A	229	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  EC: 3.4 (PDB Primary Data), 3.4.13.21 (UniProt)
UniProt
Find proteins for P36936 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P36936  Go to UniProtKB:  P36936

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.230 (Depositor) 
• R-Value Work:  0.218 (Depositor), 0.216 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.986	α = 90
b = 42.69	β = 106.06
c = 62.496	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-01-10 
Deposition Author(s): Hakansson, K., Wang, A.H.-J., Miller, C.G.

Revision History  

• Version 1.0: 2001-01-10
  Type: Initial release
  
• Version 1.1: 2007-10-21
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations