5VYQ | pdb_00005vyq

Crystal structure of the N-formyltransferase Rv3404c from mycobacterium tuberculosis in complex with YDP-Qui4N and folinic acid

• PDB DOI: https://doi.org/10.2210/pdb5VYQ/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis CAS/NITR204
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-26 Released: 2017-07-12 
• Deposition Author(s): Dunsirn, M.M., Thoden, J.B., Holden, H.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.200 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.167 (Depositor) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Biochemical Investigation of Rv3404c from Mycobacterium tuberculosis.

Dunsirn, M.M., Thoden, J.B., Gilbert, M., Holden, H.M.

(2017) Biochemistry 56: 3818-3825

• PubMed: 28665588 
• DOI: https://doi.org/10.1021/acs.biochem.7b00506
• Primary Citation Related Structures: 
  5VYQ


• PubMed Abstract: 
  

  The causative agent of tuberculosis, Mycobacterium tuberculosis, is a bacterium with a complex cell wall and a complicated life cycle. The genome of M. tuberculosis contains well over 4000 genes thought to encode proteins. One of these codes for a putative enzyme referred to as Rv3404c, which has attracted research attention as a potential virulence factor for over 12 years. Here we demonstrate that Rv3404c functions as a sugar N-formyltransferase that converts dTDP-4-amino-4,6-dideoxyglucose into dTDP-4-formamido-4,6-dideoxyglucose using N ¹⁰ -formyltetrahydrofolate as the carbon source. Kinetic analyses demonstrate that Rv3404c displays a significant catalytic efficiency of 1.1 × 10 ⁴ M ^-1 s ^-1 . In addition, we report the X-ray structure of a ternary complex of Rv3404c solved in the presence of N ⁵ -formyltetrahydrofolate and dTDP-4-amino-4,6-dideoxyglucose. The final model of Rv3404c was refined to an overall R-factor of 16.8% at 1.6 Å resolution. The results described herein are especially intriguing given that there have been no published reports of N-formylated sugars associated with M. tuberculosis. The data thus provide a new avenue of research into this fascinating, yet deadly, organism that apparently has been associated with human infection since ancient times.

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Organizational Affiliation: 
• Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States.
National Research Council Canada, Human Health Therapeutics, Ottawa, Ontario K1A 0R6, Canada.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 60.49 kDa 
• Atom Count: 4,585 
• Modeled Residue Count: 469 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	255	Mycobacterium tuberculosis CAS/NITR204	Mutation(s): 0  Gene Names: J113_23825 EC: 2.1.2
UniProt
Find proteins for P9WKZ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKZ3  Go to UniProtKB:  P9WKZ3

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0FX	D [auth A]	dTDP-4-amino-4,6-dideoxyglucose C16 H27 N3 O14 P2 UIVJXHWSIFBBCY-LPGAPTBISA-N
FON	C [auth A]	N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid C20 H23 N7 O7 VVIAGPKUTFNRDU-OLZOCXBDSA-N
TYD	N [auth B]	THYMIDINE-5'-DIPHOSPHATE C10 H16 N2 O11 P2 UJLXYODCHAELLY-XLPZGREQSA-N
EP1	J [auth A], R [auth B]	3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC ACID C9 H20 N2 O4 S OWXMKDGYPWMGEB-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], O [auth B], P [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	T [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	I [auth A], K [auth A], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth A], H [auth A], L [auth A], S [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
LI	M [auth A]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.200 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.167 (Depositor) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.486	α = 90
b = 73.018	β = 90
c = 173.265	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Dunsirn, M.M., Thoden, J.B., Holden, H.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115921

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2017-08-09
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description