5T2K

Geobacillus stearothermophilus HemQ with Manganese-Coproporphyrin III


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Based Mechanism for Oxidative Decarboxylation Reactions Mediated by Amino Acids and Heme Propionates in Coproheme Decarboxylase (HemQ).

Celis, A.I.Gauss, G.H.Streit, B.R.Shisler, K.Moraski, G.C.Rodgers, K.R.Lukat-Rodgers, G.S.Peters, J.W.DuBois, J.L.

(2017) J. Am. Chem. Soc. 139: 1900-1911

  • DOI: 10.1021/jacs.6b11324

  • PubMed Abstract: 
  • Coproheme decarboxylase catalyzes two sequential oxidative decarboxylations with H2O2 as the oxidant, coproheme III as substrate and cofactor, and heme b as the product. Each reaction breaks a C-C bond and results in net loss of hydride, via steps th ...

    Coproheme decarboxylase catalyzes two sequential oxidative decarboxylations with H2O2 as the oxidant, coproheme III as substrate and cofactor, and heme b as the product. Each reaction breaks a C-C bond and results in net loss of hydride, via steps that are not clear. Solution and solid-state structural characterization of the protein in complex with a substrate analog revealed a highly unconventional H2O2-activating distal environment with the reactive propionic acids (2 and 4) on the opposite side of the porphyrin plane. This suggested that, in contrast to direct C-H bond cleavage catalyzed by a high-valent iron intermediate, the coproheme oxidations must occur through mediating amino acid residues. A tyrosine that hydrogen bonds to propionate 2 in a position analogous to the substrate in ascorbate peroxidase is essential for both decarboxylations, while a lysine that salt bridges to propionate 4 is required solely for the second. A mechanism is proposed in which propionate 2 relays an oxidizing equivalent from a coproheme compound I intermediate to the reactive deprotonated tyrosine, forming Tyr•. This residue then abstracts a net hydrogen atom (H•) from propionate 2, followed by migration of the unpaired propionyl electron to the coproheme iron to yield the ferric harderoheme and CO2 products. A similar pathway is proposed for decarboxylation of propionate 4, but with a lysine residue as an essential proton shuttle. The proposed reaction suggests an extended relay of heme-mediated e-/H+ transfers and a novel route for the conversion of carboxylic acids to alkenes.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717-3400, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative heme-dependent peroxidase GT50_08830
A, B, C, D, E
248Geobacillus stearothermophilus 10Mutation(s): 0 
EC: 1.11.1.-
Find proteins for A0A0K2H9D8 (Geobacillus stearothermophilus 10)
Go to UniProtKB:  A0A0K2H9D8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
76R
Query on 76R

Download SDF File 
Download CCD File 
A, B, C, D, E
[3,3',3'',3'''-(3,8,13,17-tetramethylporphyrin-2,7,12,18-tetrayl-kappa~4~N~21~,N~22~,N~23~,N~24~)tetra(propanoato)(2-)]manganese
Manganese-Coproporphyrin III
C36 H36 Mn N4 O8
OOLOFMBJOQKFOW-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.154 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 131.016α = 90.00
b = 93.458β = 105.31
c = 132.543γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-02-08
    Type: Database references