4QVB | pdb_00004qvb

Mycobacterium tuberculosis protein Rv1155 in complex with co-enzyme F420

• PDB DOI: https://doi.org/10.2210/pdb4QVB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis 7199-99
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-14 Released: 2015-02-25 
• Deposition Author(s): Mashalidis, E.H., Gittis, A.G., Tomczak, A., Abell, C., Barry III, C.E., Garboczi, D.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.254 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.187 (Depositor) 

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

• PubMed: 25644473 
• DOI: https://doi.org/10.1002/pro.2645
• Primary Citation 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. 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.

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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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.92 kDa 
• Atom Count: 2,400 
• Modeled Residue Count: 285 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rv1155 protein	A, B	147	Mycobacterium tuberculosis 7199-99	Mutation(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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F42	M [auth B], N [auth B]	COENZYME F420 C29 H36 N5 O18 P GEHSZWRGPHDXJO-NALJQGANSA-N
PGO	L [auth A]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N
PDO	F [auth A], G [auth A], Q [auth B], R [auth B]	1,3-PROPANDIOL C3 H8 O2 YPFDHNVEDLHUCE-UHFFFAOYSA-N
EDO	H [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	C [auth A], D [auth A], E [auth A], O [auth B], P [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	S [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.254 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.579	α = 90
b = 65.172	β = 90
c = 77.063	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-25 
Deposition Author(s): Mashalidis, E.H., Gittis, A.G., Tomczak, A., Abell, C., Barry III, C.E., Garboczi, D.N.

Revision History  

• Version 1.0: 2015-02-25
  Type: Initial release
  
• Version 1.1: 2015-05-20
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations