7A9A

Crystal structure of rubredoxin B (Rv3250c) from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A new twist of rubredoxin function in M. tuberculosis.

Sushko, T.Kavaleuski, A.Grabovec, I.Kavaleuskaya, A.Vakhrameev, D.Bukhdruker, S.Marin, E.Kuzikov, A.Masamrekh, R.Shumyantseva, V.Tsumoto, K.Borshchevskiy, V.Gilep, A.Strushkevich, N.

(2021) Bioorg Chem 109: 104721-104721

  • DOI: https://doi.org/10.1016/j.bioorg.2021.104721
  • Primary Citation of Related Structures:  
    7A9A

  • PubMed Abstract: 

    Electron transfer mediated by metalloproteins drives many biological processes. Rubredoxins are a ubiquitous [1Fe-0S] class of electron carriers that play an important role in bacterial adaptation to changing environmental conditions. In Mycobacterium tuberculosis, oxidative and acidic stresses as well as iron starvation induce rubredoxins expression. However, their functions during M. tuberculosis infection are unknown. In the present work, we show that rubredoxin B (RubB) is able to efficiently shuttle electrons from cognate reductases, FprA and FdR to support catalytic activity of cytochrome P450s, CYP124, CYP125, and CYP142, which are important for bacterial viability and pathogenicity. We solved the crystal structure of RubB and characterized the interaction between RubB and CYPs using site-directed mutagenesis. Mutations that not only neutralize single charge but also change the specific residues on the surface of RubB did not dramatically decrease activity of studied CYPs. Together with isothermal calorimetry (ITC) experiments, the obtained results suggest that interactions are transient and not highly specific. The redox potential of RubB is -264 mV vs. Ag/AgCl and the measured extinction coefficients are 9931 M -1 cm -1 and 8371 M -1 cm -1 at 380 nm and 490 nm, respectively. Characteristic parameters of RubB along with the discovered function might be useful for biotechnological applications. Our findings suggest that a switch from ferredoxins to rubredoxins might be crucial for M. tuberculosis to support CYPs activity during the infection.


  • Organizational Affiliation

    The Institute of Medical Science, the University of Tokyo, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rubredoxin
A, B, C, D, E
A, B, C, D, E, F, G, H
60Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rubBRv3250c
UniProt
Find proteins for I6YFL7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6YFL7 
Go to UniProtKB:  I6YFL7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6YFL7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
IB [auth G],
KA [auth D],
OB [auth H],
RA [auth E]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth F],
BA [auth C],
PB [auth H],
ZA [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth C]
CB [auth G]
DA [auth C]
DB [auth G]
EB [auth G]
AA [auth C],
CB [auth G],
DA [auth C],
DB [auth G],
EB [auth G],
FA [auth D],
FB [auth G],
GA [auth D],
GB [auth G],
HA [auth D],
IA [auth D],
J [auth A],
JA [auth D],
JB [auth H],
K [auth A],
L [auth A],
LA [auth D],
LB [auth H],
M [auth A],
MB [auth H],
NA [auth E],
NB [auth H],
OA [auth E],
P [auth B],
PA [auth E],
Q [auth B],
QA [auth E],
R [auth B],
S [auth B],
T [auth B],
TA [auth F],
UA [auth F],
VA [auth F],
W [auth C],
WA [auth F],
X [auth C],
XA [auth F],
Y [auth C],
YA [auth F],
Z [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
HB [auth G],
N [auth A],
U [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
BB [auth G]
EA [auth D]
I [auth A]
KB [auth H]
MA [auth E]
BB [auth G],
EA [auth D],
I [auth A],
KB [auth H],
MA [auth E],
O [auth B],
SA [auth F],
V [auth C]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 21.035α = 90.152
b = 61.322β = 90.319
c = 76.91γ = 93.754
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
MoRDaphasing
STARANISOdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Foundation for Basic ResearchRussian Federation20-54-00005
Belarusian Republican Foundation for Fundamental ResearchBelarusB20R-061

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description