8AMQ

Crystal structure of the complex CYP143-FdxE from M. tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insights into 3Fe-4S ferredoxins diversity in M. tuberculosis highlighted by a first redox complex with P450.

Gilep, A.Varaksa, T.Bukhdruker, S.Kavaleuski, A.Ryzhykau, Y.Smolskaya, S.Sushko, T.Tsumoto, K.Grabovec, I.Kapranov, I.Okhrimenko, I.Marin, E.Shevtsov, M.Mishin, A.Kovalev, K.Kuklin, A.Gordeliy, V.Kaluzhskiy, L.Gnedenko, O.Yablokov, E.Ivanov, A.Borshchevskiy, V.Strushkevich, N.

(2022) Front Mol Biosci 9: 1100032-1100032

  • DOI: https://doi.org/10.3389/fmolb.2022.1100032
  • Primary Citation of Related Structures:  
    8AMO, 8AMP, 8AMQ

  • PubMed Abstract: 

    Ferredoxins are small iron-sulfur proteins and key players in essential metabolic pathways. Among all types, 3Fe-4S ferredoxins are less studied mostly due to anaerobic requirements. Their complexes with cytochrome P450 redox partners have not been structurally characterized. In the present work, we solved the structures of both 3Fe-4S ferredoxins from M. tuberculosis -Fdx alone and the fusion FdxE-CYP143. Our SPR analysis demonstrated a high-affinity binding of FdxE to CYP143. According to SAXS data, the same complex is present in solution. The structure reveals extended multipoint interactions and the shape/charge complementarity of redox partners. Furthermore, FdxE binding induced conformational changes in CYP143 as evident from the solved CYP143 structure alone. The comparison of FdxE-CYP143 and modeled Fdx-CYP51 complexes further revealed the specificity of ferredoxins. Our results illuminate the diversity of electron transfer complexes for the production of different secondary metabolites.


  • Organizational Affiliation

    Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ferredoxin,Putative cytochrome P450 143484Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv1786cyp143Rv1785cMTV049.07c
EC: 1.14
UniProt
Find proteins for O53937 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O53937 
Go to UniProtKB:  O53937
Find proteins for P9WPL3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPL3 
Go to UniProtKB:  P9WPL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP9WPL3O53937
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
F3S (Subject of Investigation/LOI)
Query on F3S

Download Ideal Coordinates CCD File 
B [auth A]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.2α = 67.71
b = 54.354β = 77.21
c = 69.037γ = 61.63
Software Package:
Software NamePurpose
XDSdata reduction
STARANISOdata scaling
PHASERphasing
PHENIXmodel building
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Higher Education of the Russian FederationRussian Federation075-15-2021-1354
Ministry of Science and Higher Education of the Russian FederationRussian Federation122030100168-2

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description