4XOO

FMN complex of coenzyme F420:L-glutamate ligase (FbiB) from Mycobacterium tuberculosis (C-terminal domain)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Elongation of the Poly-gamma-glutamate Tail of F420 Requires Both Domains of the F420: gamma-Glutamyl Ligase (FbiB) of Mycobacterium tuberculosis.

Bashiri, G.Rehan, A.M.Sreebhavan, S.Baker, H.M.Baker, E.N.Squire, C.J.

(2016) J Biol Chem 291: 6882-6894

  • DOI: 10.1074/jbc.M115.689026
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Cofactor F420is an electron carrier with a major role in the oxidoreductive reactions ofMycobacterium tuberculosis, the causative agent of tuberculosis. A γ-glutamyl ligase catalyzes the final steps of the F420biosynthesis pathway by successive addit ...

    Cofactor F420is an electron carrier with a major role in the oxidoreductive reactions ofMycobacterium tuberculosis, the causative agent of tuberculosis. A γ-glutamyl ligase catalyzes the final steps of the F420biosynthesis pathway by successive additions ofl-glutamate residues to F420-0, producing a poly-γ-glutamate tail. The enzyme responsible for this reaction in archaea (CofE) comprises a single domain and produces F420-2 as the major species. The homologousM. tuberculosisenzyme, FbiB, is a two-domain protein and produces F420with predominantly 5-7l-glutamate residues in the poly-γ-glutamate tail. The N-terminal domain of FbiB is homologous to CofE with an annotated γ-glutamyl ligase activity, whereas the C-terminal domain has sequence similarity to an FMN-dependent family of nitroreductase enzymes. Here we demonstrate that full-length FbiB adds multiplel-glutamate residues to F420-0in vitroto produce F420-5 after 24 h; communication between the two domains is critical for full γ-glutamyl ligase activity. We also present crystal structures of the C-terminal domain of FbiB in apo-, F420-0-, and FMN-bound states, displaying distinct sites for F420-0 and FMN ligands that partially overlap. Finally, we discuss the features of a full-length structural model produced by small angle x-ray scattering and its implications for the role of N- and C-terminal domains in catalysis.


    Organizational Affiliation

    From the Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, and c.squire@auckland.ac.nz.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coenzyme F420:L-glutamate ligaseA, B, C, D207Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: fbiBRv3262
EC: 6.3.2.31 (PDB Primary Data), 6.3.2.34 (PDB Primary Data), 1.3.8 (UniProt)
Find proteins for P9WP79 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WP79 
Go to UniProtKB:  P9WP79
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download CCD File 
A, B, C, D
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FMNKd:  14700   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.135α = 90
b = 137.135β = 90
c = 101.395γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-02-24
    Changes: Database references
  • Version 1.2: 2016-04-06
    Changes: Database references