8AVL

Superoxide dismutase SodFM2 from Bacteroides fragilis

PDB DOI: https://doi.org/10.2210/pdb8AVL/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacteroides fragilis YCH46
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-08-26 Released: 2023-04-19
Deposition Author(s): Basle, A., Barwinska-Sendra, A., Sendra, K.M., Waldron, K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.204
R-Value Work: 0.133

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

An ancient metalloenzyme evolves through metal preference modulation.

Sendra, K.M., Barwinska-Sendra, A., Mackenzie, E.S., Basle, A., Kehl-Fie, T.E., Waldron, K.J.

(2023) Nat Ecol Evol 7: 732-744

PubMed: 37037909 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41559-023-02012-0
Primary Citation of Related Structures:
8AVK, 8AVL, 8AVM, 8AVN

PubMed Abstract:
Evolution creates functional diversity of proteins, the essential building blocks of all biological systems. However, studies of natural proteins sampled across the tree of life and evaluated in a single experimental system are lacking. Almost half of enzymes require metals, and metalloproteins tend to optimally utilize the physicochemical properties of a specific metal co-factor. Life must adapt to changes in metal bioavailability, including those during the transition from anoxic to oxic Earth or pathogens' exposure to nutritional immunity. These changes can challenge the ability of metalloenzymes to maintain activity, presumptively driving their evolution. Here we studied metal-preference evolution within the natural diversity of the iron/manganese superoxide dismutase (SodFM) family of reactive oxygen species scavengers. We identified and experimentally verified residues with conserved roles in determining metal preference that, when combined with an understanding of the protein's evolutionary history, improved prediction of metal utilization across the five SodFM subfamilies defined herein. By combining phylogenetics, biochemistry and structural biology, we demonstrate that SodFM metal utilization can be evolutionarily fine tuned by sliding along a scale between perfect manganese and iron specificities. Over the history of life, SodFM metal preference has been modulated multiple independent times within different evolutionary and ecological contexts, and can be changed within short evolutionary timeframes.

Organizational Affiliation

Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK. kacpersendra.ncl@gmail.com.

Macromolecule Content

Total Structure Weight: 174.14 kDa
Atom Count: 13,836
Modelled Residue Count: 1,536
Deposited Residue Count: 1,536
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Fe]	A, B, C, D, E A, B, C, D, E, F, G, H	192	Bacteroides fragilis YCH46	Mutation(s): 0 Gene Names: sodB, sod, BF2527 EC: 1.15.1.1
UniProt
Find proteins for P53638 (Bacteroides fragilis (strain YCH46)) Explore P53638 Go to UniProtKB: P53638
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53638
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth E] SDF format, chain O [auth F] SDF format, chain P [auth G] SDF format, chain Q [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth E] MOL2 format, chain O [auth F] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth H]	I [auth A] K [auth B] L [auth C] M [auth D] N [auth E] I [auth A], K [auth B], L [auth C], M [auth D], N [auth E], O [auth F], P [auth G], Q [auth H]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth G] Focus chain Q [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth G] Focus chain Q [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.204
R-Value Work: 0.133
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.13	α = 90
b = 100.11	β = 91.8
c = 103.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-04-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 AI55611
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/S006818/1