3MRU

Crystal Structure of Aminoacylhistidine Dipeptidase from Vibrio alginolyticus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1074/jbc.M110.139683

  • PubMed Abstract: 
  • Aminoacylhistidine dipeptidases (PepD, EC 3.4.13.3) 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. Homocarn ...

    Aminoacylhistidine dipeptidases (PepD, EC 3.4.13.3) 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aminoacyl-histidine dipeptidase
A, B
490Vibrio alginolyticusEC: 3.4.13.18, 3.4.13.20
Find proteins for Q2LD50 (Vibrio alginolyticus)
Go to UniProtKB:  Q2LD50
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.231 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 80.407α = 90.00
b = 80.407β = 90.00
c = 303.095γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance