PDBsum entry 1fy2

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protein metals links
Hydrolase PDB id
Protein chain
220 a.a. *
Waters ×192
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Aspartyl dipeptidase
Structure: Aspartyl dipeptidase. Chain: a. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 602. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
1.20Å     R-factor:   0.218     R-free:   0.230
Authors: K.Hakansson,A.H.-J.Wang,C.G.Miller
Key ref:
K.Håkansson et al. (2000). The structure of aspartyl dipeptidase reveals a unique fold with a Ser-His-Glu catalytic triad. Proc Natl Acad Sci U S A, 97, 14097-14102. PubMed id: 11106384 DOI: 10.1073/pnas.260376797
28-Sep-00     Release date:   10-Jan-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P36936  (PEPE_SALTY) -  Peptidase E
229 a.a.
220 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Dipeptidase E.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Dipeptidase E catalyzes the hydrolysis of dipeptides Asp-|-Xaa. It does not act on peptides with N-terminal Glu, Asn or Gln, nor does it cleave isoaspartyl peptides.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     proteolysis   1 term 
  Biochemical function     hydrolase activity     4 terms  


DOI no: 10.1073/pnas.260376797 Proc Natl Acad Sci U S A 97:14097-14102 (2000)
PubMed id: 11106384  
The structure of aspartyl dipeptidase reveals a unique fold with a Ser-His-Glu catalytic triad.
K.Håkansson, A.H.Wang, C.G.Miller.
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.
  Selected figure(s)  
Figure 1.
Fig. 1. Structure of aspartyl dipeptidase. (A) Ribbon diagram (35). Helices are shown in red and -strands in blue. The side chains of the catalytic triad residues are shown in green. (B) Topological representation.
Figure 2.
Fig. 2. (A) Strand-helix motif. Superimposition of aspartyl dipeptidase (thick multicolored model) and serine carboxypeptidase (blue) illustrates similarities of the strand-helix motifs and the different histidine positions (35). The C atoms of the nine residues surrounding the active site Ser were superimposed and have a rms deviation of 0.9 Å. (B) View of the active site with Ser120 (dark gray) and the helix following it with Ala121-Asn124 (light gray). The active site Ser is coordinated to His157 and two water molecules (yellow). Glu192 is shown in green, Thr133-Asp135 in red, and Gly87-Thr90 in blue.
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18824507 O.D.Ekici, M.Paetzel, and R.E.Dalbey (2008).
Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration.
  Protein Sci, 17, 2023-2037.  
17390395 G.Füser, and A.Steinbüchel (2007).
Analysis of genome sequences for genes of cyanophycin metabolism: identifying putative cyanophycin metabolizing prokaryotes.
  Macromol Biosci, 7, 278-296.  
17879342 G.Fibriansah, S.Masuda, N.Koizumi, S.Nakamura, and T.Kumasaka (2007).
The 1.3 A crystal structure of a novel endo-beta-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96.
  Proteins, 69, 683-690.
PDB code: 2hyk
15629944 W.L.Kelly, and C.A.Townsend (2005).
Mutational analysis of nocK and nocL in the nocardicin a producer Nocardia uniformis.
  J Bacteriol, 187, 739-746.  
12896993 D.H.Broder, and C.G.Miller (2003).
DapE can function as an aspartyl peptidase in the presence of Mn2+.
  J Bacteriol, 185, 4748-4754.  
11741860 N.T.Hoa, J.A.Brannigan, and S.M.Cutting (2002).
The Bacillus subtilis signaling protein SpoIVB defines a new family of serine peptidases.
  J Bacteriol, 184, 191-199.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.