3AJE

Crystal structure of S. tokodaii Sua5 complexed with L-threonine and AMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of Sulfolobus tokodaii Sua5 complexed with L-threonine and AMPPNP

Kuratani, M.Kasai, T.Akasaka, R.Higashijima, K.Terada, T.Kigawa, T.Shinkai, A.Bessho, Y.Yokoyama, S.

(2011) Proteins 79: 2065-2075

  • DOI: 10.1002/prot.23026

  • PubMed Abstract: 
  • The hypermodified nucleoside N(6)-threonylcarbamoyladenosine resides at position 37 of tRNA molecules bearing U at position 36 and maintains translational fidelity in the three kingdoms of life. The N(6)-threonylcarbamoyl moiety is composed of L-thre ...

    The hypermodified nucleoside N(6)-threonylcarbamoyladenosine resides at position 37 of tRNA molecules bearing U at position 36 and maintains translational fidelity in the three kingdoms of life. The N(6)-threonylcarbamoyl moiety is composed of L-threonine and bicarbonate, and its synthesis was genetically shown to require YrdC/Sua5. YrdC/Sua5 binds to tRNA and ATP. In this study, we analyzed the L-threonine-binding mode of Sua5 from the archaeon Sulfolobus tokodaii. Isothermal titration calorimetry measurements revealed that S. tokodaii Sua5 binds L-threonine more strongly than L-serine and glycine. The Kd values of Sua5 for L-threonine and L-serine are 9.3 μM and 2.6 mM, respectively. We determined the crystal structure of S. tokodaii Sua5, complexed with AMPPNP and L-threonine, at 1.8 Å resolution. The L-threonine is bound next to AMPPNP in the same pocket of the N-terminal domain. Thr118 and two water molecules form hydrogen bonds with AMPPNP in a unique manner for adenine-specific recognition. The carboxyl group and the side-chain hydroxyl and methyl groups of L-threonine are buried deep in the pocket, whereas the amino group faces AMPPNP. The L-threonine is located in a suitable position to react together with ATP for the synthesis of N(6)-threonylcarbamoyladenosine.


    Organizational Affiliation

    RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein ST1526
A
352Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)Mutation(s): 0 
Gene Names: sua5
EC: 2.7.7.87
Find proteins for Q970S6 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Go to UniProtKB:  Q970S6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
THR
Query on THR

Download SDF File 
Download CCD File 
A
THREONINE
C4 H9 N O3
AYFVYJQAPQTCCC-GBXIJSLDSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
THRKd: 9300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.198 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 85.350α = 90.00
b = 121.000β = 90.00
c = 68.010γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-01-29
    Type: Database references