5LOQ

Structure of coproheme bound HemQ from Listeria monocytogenes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Hydrogen peroxide-mediated conversion of coproheme to heme b by HemQ-lessons from the first crystal structure and kinetic studies.

Hofbauer, S.Mlynek, G.Milazzo, L.Puhringer, D.Maresch, D.Schaffner, I.Furtmuller, P.G.Smulevich, G.Djinovic-Carugo, K.Obinger, C.

(2016) FEBS J 283: 4386-4401

  • DOI: https://doi.org/10.1111/febs.13930
  • Primary Citation of Related Structures:  
    5LOQ

  • PubMed Abstract: 

    Heme biosynthesis in Gram-positive bacteria follows a recently described coproporphyrin-dependent pathway with HemQ catalyzing the decarboxylation of coproheme to heme b. Here we present the first crystal structure of a HemQ (homopentameric coproheme-HemQ from Listeria monocytogenes) at 1.69 Å resolution and the conversion of coproheme to heme b followed by UV-vis and resonance Raman spectroscopy as well as mass spectrometry. The ferric five-coordinated coproheme iron of HemQ is weakly bound by a neutral proximal histidine H174. In the crystal structure of the resting state, the distal Q187 (conserved in Firmicutes HemQ) is H-bonded with propionate p2 and the hydrophobic distal cavity lacks solvent water molecules. Two H 2 O 2 molecules are shown to be necessary for decarboxylation of the propionates p2 and p4, thereby forming the corresponding vinyl groups of heme b. The overall reaction is relatively slow (k cat /K M = 1.8 × 10 2 m -1 ·s -1 at pH 7.0) and occurs in a stepwise manner with a three-propionate intermediate. We present the noncovalent interactions between coproheme and the protein and propose a two-step reaction mechanism. Furthermore, the structure of coproheme-HemQ is compared to that of the phylogenetically related heme b-containing chlorite dismutases. Structural data are available in the PDB under the accession number 5LOQ.


  • Organizational Affiliation

    Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative heme-dependent peroxidase lmo2113
A, B, C, D, E
250Listeria monocytogenesMutation(s): 0 
Gene Names: lmo2113
EC: 1.11.1
UniProt
Find proteins for Q8Y5F1 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Go to UniProtKB:  Q8Y5F1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FEC
Query on FEC

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
O [auth D],
R [auth E]
1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX
C36 H36 Fe N4 O8
FEDZMOFKVKOYTI-RGGAHWMASA-L
MPD
Query on MPD

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
P [auth D],
S [auth E]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
N [auth D],
Q [auth E]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.687α = 90
b = 129.369β = 105.52
c = 77.916γ = 90
Software Package:
Software NamePurpose
EDNAdata collection
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Database references
  • Version 1.2: 2016-12-14
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description