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PDBsum entry 1b65

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protein Protein-protein interface(s) links
Hydrolase PDB id
1b65
Jmol
Contents
Protein chains
(+ 0 more) 363 a.a. *
Waters ×1304
* Residue conservation analysis
PDB id:
1b65
Name: Hydrolase
Title: Structure of l-aminopeptidase d-ala-esterase/amidase from ochrobactrum anthropi, a prototype for the serine aminopeptidases, reveals a new variant among the ntn hydrolase fold
Structure: Protein (aminopeptidase). Chain: a, b, c, d, e, f. Synonym: dmpa. Engineered: yes
Source: Ochrobactrum anthropi. Organism_taxid: 529. Strain: lmg7991. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PDB file)
Resolution:
1.82Å     R-factor:   0.170     R-free:   0.206
Authors: C.Bompard-Gilles,V.Villeret,G.J.Davies,L.Fanuel,B.Joris, J.M.Frere,J.Van Beeumen
Key ref:
C.Bompard-Gilles et al. (2000). A new variant of the Ntn hydrolase fold revealed by the crystal structure of L-aminopeptidase D-ala-esterase/amidase from Ochrobactrum anthropi. Structure, 8, 153-162. PubMed id: 10673442 DOI: 10.1016/S0969-2126(00)00091-5
Date:
20-Jan-99     Release date:   23-Jul-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q59632  (Q59632_OCHAN) -  D-aminopeptidase
Seq:
Struc:
375 a.a.
363 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.11.19  - D-stereospecific aminopeptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Release of an N-terminal D-amino acid from a peptide, Xaa-|-Xaa-, in which Xaa is preferably D-Ala, D-Ser or D-Thr. D-amino acid amides and methyl esters also are hydrolyzed, as is glycine amide.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     hydrolase activity     2 terms  

 

 
DOI no: 10.1016/S0969-2126(00)00091-5 Structure 8:153-162 (2000)
PubMed id: 10673442  
 
 
A new variant of the Ntn hydrolase fold revealed by the crystal structure of L-aminopeptidase D-ala-esterase/amidase from Ochrobactrum anthropi.
C.Bompard-Gilles, V.Villeret, G.J.Davies, L.Fanuel, B.Joris, J.M.Frère, J.Van Beeumen.
 
  ABSTRACT  
 
Background: The L-aminopeptidase D-Ala-esterase/amidase from Ochrobactrum anthropi (DmpA) releases the N-terminal L and/or D-Ala residues from peptide substrates. This is the only known enzyme to liberate N-terminal amino acids with both D and L stereospecificity. The DmpA active form is an alphabeta heterodimer, which results from a putative autocatalytic cleavage of an inactive precursor polypeptide. Results: The crystal structure of the enzyme has been determined to 1.82 A resolution using the multiple isomorphous replacement method. The heterodimer folds into a single domain organised as an alphabetabetaalpha sandwich in which two mixed beta sheets are flanked on both sides by two alpha helices. Conclusions: DmpA shows no similarity to other known aminopeptidases in either fold or catalytic mechanism, and thus represents the first example of a novel family of aminopeptidases. The protein fold of DmpA does, however, show structural homology to members of the N-terminal nucleophile (Ntn) hydrolase superfamily. DmpA presents functionally equivalent residues in the catalytic centre when compared with other Ntn hydrolases, and is therefore likely to use the same catalytic mechanism. In spite of this homology, the direction and connectivity of the secondary structure elements differ significantly from the consensus Ntn hydrolase topology. The DmpA structure thus characterises a new subfamily, but supports the common catalytic mechanism for these enzymes suggesting an evolutionary relationship.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. The catalytic site of DmpA. (a) Stereoview electron-density map around residues of the active site of DmpA. (b) Stereoview superposition of residues involved in the catalytic mechanism of DmpA (coloured green) with those of PA (coloured by atom type) in complex with PMSF (coloured violet). (The figure was produced using the program TURBO-FRODO [43].)

 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 153-162) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20340152 T.Heck, A.Reimer, D.Seebach, J.Gardiner, G.Deniau, A.Lukaszuk, H.P.Kohler, and B.Geueke (2010).
Beta-aminopeptidase-catalyzed biotransformations of beta(2)-dipeptides: kinetic resolution and enzymatic coupling.
  Chembiochem, 11, 1129-1136.  
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.  
17318535 B.Geueke, and H.P.Kohler (2007).
Bacterial beta-peptidyl aminopeptidases: on the hydrolytic degradation of beta-peptides.
  Appl Microbiol Biotechnol, 74, 1197-1204.  
17827307 K.Yasuhira, Y.Tanaka, H.Shibata, Y.Kawashima, A.Ohara, D.Kato, M.Takeo, and S.Negoro (2007).
6-Aminohexanoate oligomer hydrolases from the alkalophilic bacteria Agromyces sp. strain KY5R and Kocuria sp. strain KY2.
  Appl Environ Microbiol, 73, 7099-7102.  
17064315 B.Geueke, T.Heck, M.Limbach, V.Nesatyy, D.Seebach, and H.P.Kohler (2006).
Bacterial beta-peptidyl aminopeptidases with unique substrate specificities for beta-oligopeptides and mixed beta,alpha-oligopeptides.
  FEBS J, 273, 5261-5272.  
15955066 H.Komeda, and Y.Asano (2005).
A DmpA-homologous protein from Pseudomonas sp. is a dipeptidase specific for beta-alanyl dipeptides.
  FEBS J, 272, 3075-3084.  
12010542 C.Pozo, B.Rodelas, S.De La Escalera, and J.González-López (2002).
D,L-Hydantoinase activity of an Ochrobactrum anthropi strain.
  J Appl Microbiol, 92, 1028-1034.  
  11206054 C.Oinonen, and J.Rouvinen (2000).
Structural comparison of Ntn-hydrolases.
  Protein Sci, 9, 2329-2337.  
10903946 T.Nakai, T.Hasegawa, E.Yamashita, M.Yamamoto, T.Kumasaka, T.Ueki, H.Nanba, Y.Ikenaka, S.Takahashi, M.Sato, and T.Tsukihara (2000).
Crystal structure of N-carbamyl-D-amino acid amidohydrolase with a novel catalytic framework common to amidohydrolases.
  Structure, 8, 729-737.
PDB code: 1erz
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.