6P78

queuine lyase from Clostridium spiroforme bound to SAM and queuine

  • Classification: LYASE
  • Organism(s): [Clostridium] spiroforme DSM 1552
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2019-06-05 Released: 2019-09-18 
  • Deposition Author(s): Almo, S.C., Grove, T.L.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 U S A 116: 19126-19135

  • DOI: 10.1073/pnas.1909604116
  • Primary Citation of Related Structures:  
    6P78

  • 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 precursor ...

    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

    University of Florida Genetics Institute, Gainesville, FL 32610.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Queuine lyaseA251[Clostridium] spiroforme DSM 1552Mutation(s): 0 
Gene Names: CLOSPI_01524
UniProt
Find proteins for B1C2R2 ([Clostridium] spiroforme DSM 1552)
Explore B1C2R2 
Go to UniProtKB:  B1C2R2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
D [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
B [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
QUG (Subject of Investigation/LOI)
Query on QUG

Download Ideal Coordinates CCD File 
C [auth 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
C12 H15 N5 O3
WYROLENTHWJFLR-ZKWXMUAHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SMC
Query on SMC
AL-PEPTIDE LINKINGC4 H9 N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.606α = 90
b = 57.606β = 90
c = 152.414γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment  



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  (Full details and data files)

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