6Z81

TsaBD bound to the inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 


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Literature

Structure of a reaction intermediate mimic in t6A biosynthesis bound in the active site of the TsaBD heterodimer from Escherichia coli.

Kopina, B.J., Missoury, S., Collinet, B., Fulton, M.G., Cirio, C., van Tilbeurgh, H., Lauhon, C.T.

(2021) Nucleic Acids Res 49: 2141-2160

  • DOI: 10.1093/nar/gkab026
  • Primary Citation of Related Structures:  
    6Z81

  • PubMed Abstract: 

    • The tRNA modification N6-threonylcarbamoyladenosine (t6A) is universally conserved in all organisms. In bacteria, the biosynthesis of t6A requires four proteins (TsaBCDE) that catalyze the formation of t6A via the unstable intermediate l-threonylcarbamoyl-adenylate (TC-AMP) ...

    The tRNA modification N6-threonylcarbamoyladenosine (t6A) is universally conserved in all organisms. In bacteria, the biosynthesis of t6A requires four proteins (TsaBCDE) that catalyze the formation of t6A via the unstable intermediate l-threonylcarbamoyl-adenylate (TC-AMP). While the formation and stability of this intermediate has been studied in detail, the mechanism of its transfer to A37 in tRNA is poorly understood. To investigate this step, the structure of the TsaBD heterodimer from Escherichia coli has been solved bound to a stable phosphonate isosteric mimic of TC-AMP. The phosphonate inhibits t6A synthesis in vitro with an IC50 value of 1.3 μM in the presence of millimolar ATP and L-threonine. The inhibitor binds to TsaBD by coordination to the active site Zn atom via an oxygen atom from both the phosphonate and the carboxylate moieties. The bound conformation of the inhibitor suggests that the catalysis exploits a putative oxyanion hole created by a conserved active site loop of TsaD and that the metal essentially serves as a binding scaffold for the intermediate. The phosphonate bound crystal structure should be useful for the rational design of potent, drug-like small molecule inhibitors as mechanistic probes or potentially novel antibiotics.

    Organizational Affiliation: 

    Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA N6-adenosine threonylcarbamoyltransferaseA, B343Escherichia coliMutation(s): 0 
Gene Names: tsaD, gcp, ygjD, b3064, JW3036
EC: 2.3.1.234
UniProt
Find proteins for P05852 (Escherichia coli (strain K12))
Explore P05852 
Go to UniProtKB:  P05852
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05852
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA threonylcarbamoyladenosine biosynthesis protein TsaBC, D237Escherichia coliMutation(s): 0 
Gene Names: tsaB, yeaZ, b1807, JW1796
UniProt
Find proteins for P76256 (Escherichia coli (strain K12))
Explore P76256 
Go to UniProtKB:  P76256
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76256
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QCB (Subject of Investigation/LOI)
Query on QCB
Download Ideal Coordinates CCD File 
H [auth A],
T [auth B]		(2~{S},3~{R})-2-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]ethanoylamino]-3-oxidanyl-butanoic acid
C16 H23 N6 O10 P
DWVLLSYZUNNOOL-JOHRSRDASA-N		 Ligand Interaction
AMP
Query on AMP
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EA [auth D],
Z [auth C]		ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N		 Ligand Interaction
PEG
Query on PEG
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N [auth A],
O [auth A],
X [auth B]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
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I [auth A],
J [auth A],
U [auth B],
V [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
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G [auth A],
S [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
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AA [auth C],
BA [auth C],
CA [auth C],
FA [auth D],
GA [auth D],
AA [auth C],
BA [auth C],
CA [auth C],
FA [auth D],
GA [auth D],
L [auth A],
M [auth A],
P [auth A],
W [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
NI
Query on NI
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E [auth A],
F [auth A],
Q [auth B],
R [auth B]		NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
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DA [auth D],
K [auth A],
Y [auth C]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.23α = 109.38
b = 69.25β = 92
c = 86.54γ = 116.94
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Database references