6N1O | pdb_00006n1o

Oxidized rat cytochrome c mutant (S47E)

• PDB DOI: https://doi.org/10.2210/pdb6N1O/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-11-09 Released: 2019-10-23 
• Deposition Author(s): Huttemann, M., Edwards, B.F.P.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.192 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.166 (Depositor) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Serine-47 phosphorylation of cytochromecin the mammalian brain regulates cytochromecoxidase and caspase-3 activity.

Kalpage, H.A., Vaishnav, A., Liu, J., Varughese, A., Wan, J., Turner, A.A., Ji, Q., Zurek, M.P., Kapralov, A.A., Kagan, V.E., Brunzelle, J.S., Recanati, M.A., Grossman, L.I., Sanderson, T.H., Lee, I., Salomon, A.R., Edwards, B.F.P., Huttemann, M.

(2019) FASEB J 33: 13503-13514

• PubMed: 31570002 
• DOI: https://doi.org/10.1096/fj.201901120R
• Primary Citation Related Structures: 
  5C0Z, 6N1O


• PubMed Abstract: 
  

  Cytochrome c (Cyt c ) is a multifunctional protein that operates as an electron carrier in the mitochondrial electron transport chain and plays a key role in apoptosis. We have previously shown that tissue-specific phosphorylations of Cyt c in the heart, liver, and kidney play an important role in the regulation of cellular respiration and cell death. Here, we report that Cyt c purified from mammalian brain is phosphorylated on S47 and that this phosphorylation is lost during ischemia. We have characterized the functional effects in vitro using phosphorylated Cyt c purified from pig brain tissue and a recombinant phosphomimetic mutant (S47E). We crystallized S47E phosphomimetic Cyt c at 1.55 Å and suggest that it spatially matches S47-phosphorylated Cyt c , making it a good model system. Both S47-phosphorylated and phosphomimetic Cyt c showed a lower oxygen consumption rate in reaction with isolated Cyt c oxidase, which we propose maintains intermediate mitochondrial membrane potentials under physiologic conditions, thus minimizing production of reactive oxygen species. S47-phosphorylated and phosphomimetic Cyt c showed lower caspase-3 activity. Furthermore, phosphomimetic Cyt c had decreased cardiolipin peroxidase activity and is more stable in the presence of H ₂ O ₂ . Our data suggest that S47 phosphorylation of Cyt c is tissue protective and promotes cell survival in the brain.-Kalpage, H. A., Vaishnav, A., Liu, J., Varughese, A., Wan, J., Turner, A. A., Ji, Q., Zurek, M. P., Kapralov, A. A., Kagan, V. E., Brunzelle, J. S., Recanati, M.-A., Grossman, L. I., Sanderson, T. H., Lee, I., Salomon, A. R., Edwards, B. F. P, Hüttemann, M. Serine-47 phosphorylation of cytochrome c in the mammalian brain regulates cytochrome c oxidase and caspase-3 activity.

---

Organizational Affiliation: 
• Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA.
Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, Michigan, USA.
Department of Chemistry, Brown University, Providence, Rhode Island, USA.
Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
Laboratory of Navigational Redox Lipidomics, I. M. Sechenov Moscow Medical State University, Moscow, Russia.
Center for Synchrotron Research, Northwestern University, Argonne, Illinois, USA.
Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, USA.
Department of Emergency Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA.
Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA.
Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, Michigan, USA.
College of Medicine, Dankook University, Cheonan-si, South Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.6 kDa 
• Atom Count: 3,819 
• Modeled Residue Count: 416 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c, somatic	A, B, C, D	104	Rattus norvegicus	Mutation(s): 1  Gene Names: Cycs
UniProt
Find proteins for P62898 (Rattus norvegicus) Explore P62898  Go to UniProtKB:  P62898

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	E [auth A], I [auth B], L [auth C], N [auth D]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
FC6	H [auth A], J [auth B], K [auth B], M [auth C]	HEXACYANOFERRATE(3-) C6 Fe N6 HCMVSLMENOCDCK-UHFFFAOYSA-N
EDO	F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.192 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.166 (Depositor) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.705	α = 109.89
b = 52.357	β = 92.66
c = 61.819	γ = 91.15

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-10-23 
Deposition Author(s): Huttemann, M., Edwards, B.F.P.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GM1166807

Revision History  

• Version 1.0: 2019-10-23
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary