6P78

queuine lyase from Clostridium spiroforme bound to SAM and queuine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.726 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens.

Yuan, Y.Zallot, R.Grove, T.L.Payan, D.J.Martin-Verstraete, I.Sepic, S.Balamkundu, S.Neelakandan, R.Gadi, V.K.Liu, C.F.Swairjo, M.A.Dedon, P.C.Almo, S.C.Gerlt, J.A.de Crecy-Lagard, V.

(2019) Proc.Natl.Acad.Sci.USA 116: 19126-19135

  • DOI: 10.1073/pnas.1909604116

  • PubMed Abstract: 
  • Queuosine (Q) is a complex tRNA modification widespread in eukaryotes and bacteria that contributes to the efficiency and accuracy of protein synthesis. Eukaryotes are not capable of Q synthesis and rely on salvage of the queuine base (q) as a Q prec ...

    Queuosine (Q) is a complex tRNA modification widespread in eukaryotes and bacteria that contributes to the efficiency and accuracy of protein synthesis. Eukaryotes are not capable of Q synthesis and rely on salvage of the queuine base (q) as a Q precursor. While many bacteria are capable of Q de novo synthesis, salvage of the prokaryotic Q precursors preQ 0 and preQ 1 also occurs. With the exception of Escherichia coli YhhQ, shown to transport preQ 0 and preQ 1 , the enzymes and transporters involved in Q salvage and recycling have not been well described. We discovered and characterized 2 Q salvage pathways present in many pathogenic and commensal bacteria. The first, found in the intracellular pathogen Chlamydia trachomatis , uses YhhQ and tRNA guanine transglycosylase (TGT) homologs that have changed substrate specificities to directly salvage q, mimicking the eukaryotic pathway. The second, found in bacteria from the gut flora such as Clostridioides difficile , salvages preQ 1 from q through an unprecedented reaction catalyzed by a newly defined subgroup of the radical-SAM enzyme family. The source of q can be external through transport by members of the energy-coupling factor (ECF) family or internal through hydrolysis of Q by a dedicated nucleosidase. This work reinforces the concept that hosts and members of their associated microbiota compete for the salvage of Q precursors micronutrients.


    Organizational Affiliation

    Department of Biological Engineering and Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139.,Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801.,University of Florida Genetics Institute, Gainesville, FL 32610.,Laboratoire de Pathogénèse des Bactéries Anaérobies, Institut Pasteur et Université de Paris, F-75015 Paris, France.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139.,Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801.,Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611; vcrecy@ufl.edu.,Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611.,The Viral Information Institute, San Diego State University, San Diego, CA 92182.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801.,Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Queuine lyase
A
251[Clostridium] spiroforme DSM 1552Mutation(s): 0 
Find proteins for B1C2R2 ([Clostridium] spiroforme DSM 1552)
Go to UniProtKB:  B1C2R2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
QUG
Query on QUG

Download SDF File 
Download CCD File 
A
2-amino-5-({[(1S,4S,5S)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-1,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
Queuine
C12 H15 N5 O3
WYROLENTHWJFLR-ZKWXMUAHSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SMC
Query on SMC
A
L-PEPTIDE LINKINGC4 H9 N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.726 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.165 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.606α = 90.00
b = 57.606β = 90.00
c = 152.414γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
AutoSolphasing
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI133329
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54-GM093342

Revision History 

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-02
    Type: Data collection, Database references
  • Version 1.2: 2019-12-18
    Type: Author supporting evidence