4QVB

Mycobacterium tuberculosis protein Rv1155 in complex with co-enzyme F420


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Molecular insights into the binding of coenzyme F420 to the conserved protein Rv1155 from Mycobacterium tuberculosis.

Mashalidis, E.H.Gittis, A.G.Tomczak, A.Abell, C.Barry, C.E.Garboczi, D.N.

(2015) Protein Sci 24: 729-740

  • DOI: 10.1002/pro.2645
  • Primary Citation of Related Structures:  
    4QVB

  • PubMed Abstract: 
  • Coenzyme F420 is a deazaflavin hydride carrier with a lower reduction potential than most flavins. In Mycobacterium tuberculosis (Mtb), F420 plays an important role in activating PA-824, an antituberculosis drug currently used in clinical trials. Although F420 is important to Mtb redox metabolism, little is known about the enzymes that bind F420 and the reactions that they catalyze ...

    Coenzyme F420 is a deazaflavin hydride carrier with a lower reduction potential than most flavins. In Mycobacterium tuberculosis (Mtb), F420 plays an important role in activating PA-824, an antituberculosis drug currently used in clinical trials. Although F420 is important to Mtb redox metabolism, little is known about the enzymes that bind F420 and the reactions that they catalyze. We have identified a novel F420 -binding protein, Rv1155, which is annotated in the Mtb genome sequence as a putative flavin mononucleotide (FMN)-binding protein. Using biophysical techniques, we have demonstrated that instead of binding FMN or other flavins, Rv1155 binds coenzyme F420 . The crystal structure of the complex of Rv1155 and F420 reveals one F420 molecule bound to each monomer of the Rv1155 dimer. Structural, biophysical, and bioinformatic analyses of the Rv1155-F420 complex provide clues about its role in the bacterium.


    Organizational Affiliation

    Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, 20892; Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Rv1155 proteinA, B147Mycobacterium tuberculosis 7199-99Mutation(s): 0 
Gene Names: MT7199_1184
EC: 1
UniProt
Find proteins for O06553 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O06553 
Go to UniProtKB:  O06553
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F42 (Subject of Investigation/LOI)
Query on F42

Download Ideal Coordinates CCD File 
M [auth B], N [auth B]COENZYME F420
C29 H36 N5 O18 P
GEHSZWRGPHDXJO-NALJQGANSA-N
 Ligand Interaction
PGO
Query on PGO

Download Ideal Coordinates CCD File 
L [auth A]S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
PDO
Query on PDO

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], Q [auth B], R [auth B]1,3-PROPANDIOL
C3 H8 O2
YPFDHNVEDLHUCE-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], J [auth A], K [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], O [auth B], P [auth B]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
S [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
F42 Binding MOAD:  4QVB Kd: 1.70e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.579α = 90
b = 65.172β = 90
c = 77.063γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
MOLREPphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-05-20
    Changes: Database references