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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.3389/fcimb.2020.00156
  • Structures With Same Primary Citation

  • 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 me ...

    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.


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipoate--protein ligase
A, B
351Mycoplasma hyopneumoniae JMutation(s): 0 
Gene Names: lplA-1MHJ_0302
EC: 6.3.1.20
Find proteins for Q4AA29 (Mycoplasma hyopneumoniae (strain J / ATCC 25934 / NCTC 10110))
Go to UniProtKB:  Q4AA29
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LAQ
Query on LAQ

Download CCD File 
A, 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
 Ligand Interaction
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references