Crystal structure of Lysine decarboxylase from Selenomonas ruminantium in P43212 space group

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.203 

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This is version 1.3 of the entry. See complete history


Crystal Structure and Pyridoxal 5-Phosphate Binding Property of Lysine Decarboxylase from Selenomonas ruminantium

Sagong, H.-Y.Son, H.F.Kim, S.Kim, Y.-H.Kim, I.-K.Kim, K.-J.

(2016) PLoS One 11: e0166667-e0166667

  • DOI: https://doi.org/10.1371/journal.pone.0166667
  • Primary Citation of Related Structures:  
    5GJM, 5GJN, 5GJP

  • PubMed Abstract: 

    Lysine decarboxylase (LDC) is a crucial enzyme for acid stress resistance and is also utilized for the biosynthesis of cadaverine, a promising building block for bio-based polyamides. We determined the crystal structure of LDC from Selenomonas ruminantium (SrLDC). SrLDC functions as a dimer and each monomer consists of two distinct domains; a PLP-binding barrel domain and a sheet domain. We also determined the structure of SrLDC in complex with PLP and cadaverine and elucidated the binding mode of cofactor and substrate. Interestingly, compared with the apo-form of SrLDC, the SrLDC in complex with PLP and cadaverine showed a remarkable structural change at the PLP binding site. The PLP binding site of SrLDC contains the highly flexible loops with high b-factors and showed an open-closed conformational change upon the binding of PLP. In fact, SrLDC showed no LDC activity without PLP supplement, and we suggest that highly flexible PLP binding site results in low PLP affinity of SrLDC. In addition, other structurally homologous enzymes also contain the flexible PLP binding site, which indicates that high flexibility at the PLP binding site and low PLP affinity seems to be a common feature of these enzyme family.

  • Organizational Affiliation

    School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 689-798, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine/ornithine decarboxylase393Selenomonas ruminantiumMutation(s): 0 
Gene Names: ldc
EC: (PDB Primary Data), (UniProt)
Find proteins for O50657 (Selenomonas ruminantium)
Explore O50657 
Go to UniProtKB:  O50657
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO50657
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.203 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.966α = 90
b = 105.966β = 90
c = 73.634γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2017-07-19
    Changes: Database references, Derived calculations
  • Version 1.2: 2020-09-09
    Changes: Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description