2XMO

The crystal structure of Lmo2642

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structural and Functional Analysis of the Lmo2642 Cyclic Nucleotide Phosphodiesterase from Listeria Monocytogenes.

Kim, Y.G., Jeong, J.H., Ha, N.C., Kim, K.J.

(2011) Proteins 79: 1205

  • DOI: 10.1002/prot.22954

  • PubMed Abstract: 

    • Listeria monocytogenes is a facultative intracellular pathogen invading humans and animals with the highest fatality rate among the food-borne pathogens. The Listeria pathogenic processes, such as cell entry and escape from phagosomes, depend on the ...

    Listeria monocytogenes is a facultative intracellular pathogen invading humans and animals with the highest fatality rate among the food-borne pathogens. The Listeria pathogenic processes, such as cell entry and escape from phagosomes, depend on the actions of diverse bacterial factors, including lipoproteins. Here, we report the crystal structure of Lmo2642, a conserved putative lipoprotein containing a Ser/Thr phosphatase domain. The protein consists of two distinct domains: a catalytic domain that belongs to the metallophosphoesterase superfamily and an auxiliary α-helical bundle domain. The active site in the catalytic domain of Lmo2642 contains a dinuclear metal center in which Mn²(+) and Fe³(+) are preferentially positioned at the site1 and site2, respectively. On the basis of the structural analysis and enzymatic assays, we identified the biochemical activity of the protein as a cyclic nucleotide phosphodiesterase toward 2',3'- and 3',5'-cyclic nucleotides. Considering the cNMP phosphodiesterase activity and the putative surface localization of Lmo2642, we speculate that Lmo2642 has some potential roles in the host-pathogen interactions by changing the cAMP concentration of host cells during L. monocytogenes infection.

    Organizational Affiliation: 

    Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Republic of Korea. ygkim76@postech.ac.kr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LMO2642 PROTEIN
A, B
443Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)Mutation(s): 0 
Find proteins for Q8Y432 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Go to UniProtKB:  Q8Y432
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN
Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4
Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE
Download SDF File 
Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.963α = 90.00
b = 103.267β = 102.80
c = 73.765γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2010-07-28 
  • Released Date: 2011-02-23 
  • Deposition Author(s): Jeong, J.H., Kim, Y.G.

Revision History 

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-06-02
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance