6JOM

Crystal structure of lipoate protein ligase from Mycoplasma hyopneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

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This is version 1.2 of the entry. See complete history


Literature

Functional Identification and Structural Analysis of a New Lipoate Protein Ligase inMycoplasma hyopneumoniae.

Zhu, K.Chen, H.Jin, J.Wang, N.Ma, G.Huang, J.Feng, Y.Xin, J.Zhang, H.Liu, H.

(2020) Front Cell Infect Microbiol 10: 156-156

  • DOI: https://doi.org/10.3389/fcimb.2020.00156
  • Primary Citation of Related Structures:  
    6JOM

  • PubMed Abstract: 

    Mycoplasma hyopneumoniae ( M. hyopneumoniae ) is the causative agent of pandemic pneumonia among pigs, namely, swine enzootic pneumonia. Although M. hyopneumoniae was first identified in 1965, little is known regarding its metabolic pathways, which might play a pivotal role during disease pathogenesis. Lipoate is an essential cofactor for enzymes important for central metabolism. However, the lipoate metabolism pathway in M. hyopneumoniae is definitely unclear. Here, we identified a novel gene, lpl, encoding a lipoate protein ligase in the genome of M. hyopneumoniae (Mhp-Lpl). This gene contains 1,032 base pairs and encodes a protein of 343 amino acids, which is between 7.5 and 36.09% identical to lipoate protein ligases (Lpls) of other species. Similar to its homologs in other species, Mhp-Lpl catalyzes the ATP-dependent activation of lipoate to lipoyl-AMP and the transfer of the activated lipoyl onto the lipoyl domains of M. hyopneumoniae GcvH (Mhp H) in vitro . Enzymatic and mutagenesis analysis indicate that residue K56 within the SKT sequence of Mhp H protein is the lipoyl moiety acceptor site. The three-dimensional structure showed typical lipoate protein ligase folding, with a large N-terminal domain and a small C-terminal domain. The large N-terminal domain is responsible for the full enzymatic activity of Mhp-Lpl. The identification and characterization of Mhp-Lpl will be beneficial to our understanding of M. hyopneumoniae metabolism. Lipoic acid is an essential cofactor for the activation of some enzyme complexes involved in key metabolic processes. Lipoate protein ligases (Lpls) are responsible for the metabolism of lipoic acid. To date, little is known regarding the Lpls in M. hyopneumoniae . In this study, we identified a lipoate protein ligase of M. hyopneumoniae . We further analyzed the function, overall structure and ligand-binding site of this protein. The lipoate acceptor site on M. hyopneumoniae GcvH was also identified. Together, these findings reveal that Lpl exists in M. hyopneumoniae and will provide a basis for further exploration of the pathway of lipoic acid metabolism in M. hyopneumoniae .


  • Organizational Affiliation

    State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipoate--protein ligase
A, B
351Mesomycoplasma hyopneumoniae JMutation(s): 0 
Gene Names: lplA-1
EC: 6.3.1.20
UniProt
Find proteins for Q4AA29 (Mesomycoplasma hyopneumoniae (strain J / ATCC 25934 / NCTC 10110))
Explore Q4AA29 
Go to UniProtKB:  Q4AA29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4AA29
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LAQ
Query on LAQ

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
5'-O-[(R)-({5-[(3R)-1,2-DITHIOLAN-3-YL]PENTANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE
C18 H26 N5 O8 P S2
QWEGOCJRZOKSOE-ADUAKINBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.322α = 90
b = 100.322β = 90
c = 155.587γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
SHELXphasing
DMphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Refinement description