7Q4G

Structure of coproheme decarboxylase from Corynebacterium dipththeriae Y135A mutant in complex with coproheme

• PDB DOI: https://doi.org/10.2210/pdb7Q4G/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Corynebacterium diphtheriae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-10-30 Released: 2022-02-23 
• Deposition Author(s): Michlits, H., Valente, N., Mlynek, G., Hofbauer, S.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.219 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Literature

Initial Steps to Engineer Coproheme Decarboxylase to Obtain Stereospecific Monovinyl, Monopropionyl Deuterohemes.

Michlits, H., Valente, N., Mlynek, G., Hofbauer, S.

(2021) Front Bioeng Biotechnol 9: 807678-807678

• PubMed: 35141216 
• DOI: https://doi.org/10.3389/fbioe.2021.807678
• Primary Citation of Related Structures:  
  7Q4F, 7Q4G


• PubMed Abstract: 
  

  The oxidative decarboxylation of coproheme to form heme b by coproheme decarboxylase is a stereospecific two-step reaction. In the first step, the propionate at position two (p2) is cleaved off the pyrrole ring A to form a vinyl group at this position. Subsequently, the propionate at position four (p4) on pyrrole ring B is cleaved off and heme b is formed. In this study, we attempted to engineer coproheme decarboxylase from Corynebacterium diphtheriae to alter the stereospecificity of this reaction. By introducing a tyrosine residue in proximity to the propionate at position 4, we were able to create a new radical center in the active site. However, the artificial Tyr183 ^• radical could not be shown to catalyze any decarboxylation.

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Organizational Affiliation: 

Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 139.63 kDa 
• Atom Count: 10,503 
• Modelled Residue Count: 1,149 
• Deposited Residue Count: 1,185 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coproheme decarboxylase from Corynebacterium diphtheriae Y135A mutant in complex with coproheme	A, B, C, D, E	237	Corynebacterium diphtheriae	Mutation(s): 1  Gene Names: BT093_04375
UniProt
Find proteins for Q6NGV6 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NGV6  Go to UniProtKB:  Q6NGV6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FEC (Subject of Investigation/LOI)	F [auth A], G [auth B], H [auth C], J [auth D], K [auth E]	1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX C36 H36 Fe N4 O8 FEDZMOFKVKOYTI-RGGAHWMASA-L
PEG	I [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.219 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.117	α = 90
b = 123.517	β = 98.02
c = 78.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PDB-REDO	refinement
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-23 
Deposition Author(s): Michlits, H., Valente, N., Mlynek, G., Hofbauer, S.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P29099

Revision History  

• Version 1.0: 2022-02-23
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description