6FXQ

Structure of coproheme decarboxylase from Listeria monocytogenes during turnover


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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Literature

Redox Cofactor Rotates during Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Hemeb.

Milazzo, L.Gabler, T.Puhringer, D.Jandova, Z.Maresch, D.Michlits, H.Pfanzagl, V.Djinovic-Carugo, K.Oostenbrink, C.Furtmuller, P.G.Obinger, C.Smulevich, G.Hofbauer, S.

(2019) ACS Catal 9: 6766-6782

  • DOI: 10.1021/acscatal.9b00963
  • Primary Citation of Related Structures:  
    6FXQ, 6FXJ

  • PubMed Abstract: 
  • Coproheme decarboxylase (ChdC) catalyzes the last step in the heme biosynthesis pathway of monoderm bacteria with coproheme acting both as redox cofactor and substrate. Hydrogen peroxide mediates the stepwise decarboxylation of propionates 2 and 4 of coproheme ...

    Coproheme decarboxylase (ChdC) catalyzes the last step in the heme biosynthesis pathway of monoderm bacteria with coproheme acting both as redox cofactor and substrate. Hydrogen peroxide mediates the stepwise decarboxylation of propionates 2 and 4 of coproheme. Here we present the crystal structures of coproheme-loaded ChdC from Listeria monocytogenes (LmChdC) and the three-propionate intermediate, for which the propionate at position 2 (p2) has been converted to a vinyl group and is rotated by 90° compared to the coproheme complex structure. Single, double, and triple mutants of LmChdC, in which H-bonding interactions to propionates 2, 4, 6, and 7 were eliminated, allowed us to obtain the assignment of the coproheme propionates by resonance Raman spectroscopy and to follow the H 2 O 2 -mediated conversion of coproheme to heme b . Substitution of H 2 O 2 by chlorite allowed us to monitor compound I formation in the inactive Y147H variant which lacks the catalytically essential Y147. This residue was demonstrated to be oxidized during turnover by using the spin-trap 2-methyl-2-nitrosopropane. Based on these findings and the data derived from molecular dynamics simulations of cofactor structures in distinct poses, we propose a reaction mechanism for the stepwise decarboxylation of coproheme that includes a 90° rotation of the intermediate three-propionate redox cofactor.


    Organizational Affiliation

    Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative heme-dependent peroxidase lmo2113A, B, C, D, E250Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: lmo2113chdChemQ
EC: 1.11.1 (PDB Primary Data), 1.3.98.5 (UniProt)
UniProt
Find proteins for Q8Y5F1 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore Q8Y5F1 
Go to UniProtKB:  Q8Y5F1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FEC (Subject of Investigation/LOI)
Query on FEC

Download Ideal Coordinates CCD File 
G [auth A], L [auth B], O [auth C], R [auth D], V [auth E]1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX
C36 H36 Fe N4 O8
FEDZMOFKVKOYTI-RGGAHWMASA-L
 Ligand Interaction
VOV (Subject of Investigation/LOI)
Query on VOV

Download Ideal Coordinates CCD File 
H [auth A], M [auth B], P [auth C], S [auth D], W [auth E]harderoheme (III)
C35 H34 Fe N4 O6
WHUQBNXBFVNCIJ-RGGAHWMASA-L
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
I [auth A], N [auth B], T [auth D], X [auth E](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A], J [auth A], K [auth B], Q [auth C], U [auth D]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • 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
xia2data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaP29099

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-08-28
    Changes: Data collection, Database references