8FM6 | pdb_00008fm6

Dri1 hemoprotein variant H21A with a zinc-mirror heme site

• PDB DOI: https://doi.org/10.2210/pdb8FM6/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Synechocystis sp. PCC 6803
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-12-22 Released: 2024-04-24 
• Deposition Author(s): Yee, E.F., Blaby-Haas, C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.271 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria.

Grosjean, N., Yee, E.F., Kumaran, D., Chopra, K., Abernathy, M., Biswas, S., Byrnes, J., Kreitler, D.F., Cheng, J.F., Ghosh, A., Almo, S.C., Iwai, M., Niyogi, K.K., Pakrasi, H.B., Sarangi, R., van Dam, H., Yang, L., Blaby, I.K., Blaby-Haas, C.E.

(2024) Nat Commun 15: 3167-3167

• PubMed: 38609367 
• DOI: https://doi.org/10.1038/s41467-024-47486-z
• Primary Citation Related Structures: 
  8FM6, 8GBK, 8GDW, 8GF4


• PubMed Abstract: 
  

  Heme has a critical role in the chemical framework of the cell as an essential protein cofactor and signaling molecule that controls diverse processes and molecular interactions. Using a phylogenomics-based approach and complementary structural techniques, we identify a family of dimeric hemoproteins comprising a domain of unknown function DUF2470. The heme iron is axially coordinated by two zinc-bound histidine residues, forming a distinct two-fold symmetric zinc-histidine-iron-histidine-zinc site. Together with structure-guided in vitro and in vivo experiments, we further demonstrate the existence of a functional link between heme binding by Dri1 (Domain related to iron 1, formerly ssr1698) and post-translational regulation of succinate dehydrogenase in the cyanobacterium Synechocystis, suggesting an iron-dependent regulatory link between photosynthesis and respiration. Given the ubiquity of proteins containing homologous domains and connections to heme metabolism across eukaryotes and prokaryotes, we propose that DRI (Domain Related to Iron; formerly DUF2470) functions at the molecular level as a heme-dependent regulatory domain.

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Organizational Affiliation: 
• Biology Department, Brookhaven National Laboratory, Upton, NY, USA.
US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA.
Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, USA.
Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
Department of Biology, Washington University, St. Louis, MO, USA.
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA.
Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, USA.
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Biology Department, Brookhaven National Laboratory, Upton, NY, USA. [e-mail].
US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [e-mail].
The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 23.1 kDa 
• Atom Count: 1,523 
• Modeled Residue Count: 196 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ssr1698 protein	A, B	103	Synechocystis sp. PCC 6803	Mutation(s): 1  Gene Names: ssr1698
UniProt
Find proteins for P73129 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P73129  Go to UniProtKB:  P73129

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEB (Subject of Investigation/LOI)	C [auth A]	HEME B/C C34 H34 Fe N4 O4 NEGHHAJBRZGUAY-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.271 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.659	α = 90
b = 74.659	β = 90
c = 211.188	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
Aimless	data scaling
XDS	data reduction
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Yee, E.F., Blaby-Haas, C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release