Crystal Structure of Aminoacylhistidine Dipeptidase from Vibrio alginolyticus

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.231 

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Crystal structure and mutational analysis of aminoacylhistidine dipeptidase from vibrio alginolyticus reveal a new architecture of M20 metallopeptidases

Chang, C.-Y.Hsieh, Y.-C.Wang, T.-Y.Chen, Y.-C.Wang, Y.-K.Chiang, T.-W.Chen, Y.-J.Chang, C.-H.Chen, C.-J.Wu, T.-K.

(2010) J Biol Chem 285: 39500-39510

  • DOI: https://doi.org/10.1074/jbc.M110.139683
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Aminoacylhistidine dipeptidases (PepD, EC belong to the family of M20 metallopeptidases from the metallopeptidase H clan that catalyze a broad range of dipeptide and tripeptide substrates, including L-carnosine and L-homocarnosine. Homocarnosine has been suggested as a precursor for the neurotransmitter γ-aminobutyric acid (GABA) and may mediate the antiseizure effects of GABAergic therapies. Here, we report the crystal structure of PepD from Vibrio alginolyticus and the results of mutational analysis of substrate-binding residues in the C-terminal as well as substrate specificity of the PepD catalytic domain-alone truncated protein PepD(CAT). The structure of PepD was found to exist as a homodimer, in which each monomer comprises a catalytic domain containing two zinc ions at the active site center for its hydrolytic function and a lid domain utilizing hydrogen bonds between helices to form the dimer interface. Although the PepD is structurally similar to PepV, which exists as a monomer, putative substrate-binding residues reside in different topological regions of the polypeptide chain. In addition, the lid domain of the PepD contains an "extra" domain not observed in related M20 family metallopeptidases with a dimeric structure. Mutational assays confirmed both the putative di-zinc allocations and the architecture of substrate recognition. In addition, the catalytic domain-alone truncated PepD(CAT) exhibited substrate specificity to l-homocarnosine compared with that of the wild-type PepD, indicating a potential value in applications of PepD(CAT) for GABAergic therapies or neuroprotection.

  • Organizational Affiliation

    Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoacyl-histidine dipeptidase
A, B
490Vibrio alginolyticusMutation(s): 0 
Find proteins for Q2LD50 (Vibrio alginolyticus)
Explore Q2LD50 
Go to UniProtKB:  Q2LD50
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2LD50
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.231 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.407α = 90
b = 80.407β = 90
c = 303.095γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description