6RWV | pdb_00006rwv

Structure of apo-LmCpfC

• PDB DOI: https://doi.org/10.2210/pdb6RWV/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Listeria monocytogenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-06-06 Released: 2019-12-18 
• Deposition Author(s): Hofbauer, S., Helm, J., Djinovic-Carugo, K., Furtmueller, P.G.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.201 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structures and calorimetry reveal catalytically relevant binding mode of coproporphyrin and coproheme in coproporphyrin ferrochelatase.

Hofbauer, S., Helm, J., Obinger, C., Djinovic-Carugo, K., Furtmuller, P.G.

(2020) FEBS J 287: 2779-2796

• PubMed: 31794133 
• DOI: https://doi.org/10.1111/febs.15164
• Primary Citation Related Structures: 
  6RWV, 6SV3


• PubMed Abstract: 
  

  Coproporphyrin ferrochelatases (CpfCs, EC 4.99.1.9) insert ferrous iron into coproporphyrin III yielding coproheme. CpfCs are utilized by prokaryotic, mainly monoderm (Gram-positive) bacteria within the recently detected coproporphyrin-dependent (CPD) heme biosynthesis pathway. Here, we present a comprehensive study on CpfC from Listeria monocytogenes (LmCpfC) including the first crystal structure of a coproheme-bound CpfC. Comparison of crystal structures of apo-LmCpfC and coproheme-LmCpfC allowed identification of structural rearrangements and of amino acids involved in tetrapyrrole macrocycle and Fe ²⁺ binding. Differential scanning calorimetry of apo-, coproporphyrin III-, and coproheme-LmCpfC underline the pronounced noncovalent interaction of both coproporphyrin and coproheme with the protein (ΔT _m  = 11 °C compared to apo-LmCpfC), which includes the propionates (p2, p4, p6, p7) and the amino acids Arg29, Arg45, Tyr46, Ser53, and Tyr124. Furthermore, the thermodynamics and kinetics of coproporphyrin III and coproheme binding to apo-LmCpfC is presented as well as the kinetics of insertion of ferrous iron into coproporphyrin III-LmCpfC that immediately leads to formation of ferric coproheme-LmCpfC (k _cat /K _M  = 4.7 × 10 ⁵  m ^-1 ·s ^-1 ). We compare the crystal structure of coproheme-LmCpfC with available structures of CpfCs with artificial tetrapyrrole macrocycles and discuss our data on substrate binding, iron insertion and substrate release in the context of the CPD heme biosynthesis pathway. ENZYME: EC 4.99.1.9 DATABASE: pdb-codes of structural data in this work: 6RWV, 6SV3.

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Organizational Affiliation: 
• Department of Chemistry, Institute of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria.
Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Austria.
Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Slovenia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 36.68 kDa 
• Atom Count: 2,887 
• Modeled Residue Count: 310 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferrochelatase	A	312	Listeria monocytogenes	Mutation(s): 0  Gene Names:  hemH, A4G43_07995, AF115_13645, AP101_13400, AP103_13395, AP112_12715, AP127_13135, AP130_13225, APD66_13050, ARS86_05675, B1N21_11380, B4Y57_13635, B5G78_12175, B5H07_07285, BRS71_03785, D3X95_05200, D3Y03_05130, D8K64_06195, EAJ22_07595, EAX63_13360, EFX44_12300, SG10_07760 EC: 4.99.1.1 (PDB Primary Data), 4.99.1.9 (UniProt)
UniProt
Find proteins for Q8Y565 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y565  Go to UniProtKB:  Q8Y565

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	I [auth A], J [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	K [auth A], L [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.201 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.303	α = 90
b = 76.723	β = 106.558
c = 52.258	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-12-18 
Deposition Author(s): Hofbauer, S., Helm, J., Djinovic-Carugo, K., Furtmueller, P.G.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P29099

Revision History  

• Version 1.0: 2019-12-18
  Type: Initial release
  
• Version 1.1: 2020-07-15
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description