5T2K

Geobacillus stearothermophilus HemQ with Manganese-Coproporphyrin III


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

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
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Coproheme decarboxylase catalyzes two sequential oxidative decarboxylations with H 2 O 2 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 los ...

    Coproheme decarboxylase catalyzes two sequential oxidative decarboxylations with H 2 O 2 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 H 2 O 2 -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 CO 2 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_08830A, B, C, D, E248Geobacillus stearothermophilus 10Mutation(s): 0 
Gene Names: GT50_08830chdC
EC: 1.11.1 (PDB Primary Data), 1.3.98.5 (UniProt)
Find proteins for A0A0K2H9D8 (Geobacillus stearothermophilus (strain DSM 13240 / CIP 106956 / 10))
Explore A0A0K2H9D8 
Go to UniProtKB:  A0A0K2H9D8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
76R
Query on 76R

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
C36 H36 Mn N4 O8
OOLOFMBJOQKFOW-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.016α = 90
b = 93.458β = 105.31
c = 132.543γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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