3AMU

Crystal structure of the TiaS-tRNA(Ile2)-AMPCPP-agmatine complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 

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Literature

Structural basis of tRNA agmatinylation essential for AUA codon decoding

Osawa, T.Kimura, S.Terasaka, N.Inanaga, H.Suzuki, T.Numata, T.

(2011) Nat Struct Mol Biol 18: 1275-1280

  • DOI: 10.1038/nsmb.2144
  • Primary Citation of Related Structures:  
    3AMT, 3AMU, 3AU7

  • PubMed Abstract: 
  • The cytidine at the first position of the anticodon (C34) in the AUA codon-specific archaeal tRNA(Ile2) is modified to 2-agmatinylcytidine (agm(2)C or agmatidine), an agmatine-conjugated cytidine derivative, which is crucial for the precise decoding of the genetic code ...

    The cytidine at the first position of the anticodon (C34) in the AUA codon-specific archaeal tRNA(Ile2) is modified to 2-agmatinylcytidine (agm(2)C or agmatidine), an agmatine-conjugated cytidine derivative, which is crucial for the precise decoding of the genetic code. Agm(2)C is synthesized by tRNA(Ile)-agm(2)C synthetase (TiaS) in an ATP-dependent manner. Here we present the crystal structures of the Archaeoglobus fulgidus TiaS-tRNA(Ile2) complexed with ATP, or with AMPCPP and agmatine, revealing a previously unknown kinase module required for activating C34 by phosphorylation, and showing the molecular mechanism by which TiaS discriminates between tRNA(Ile2) and tRNA(Met). In the TiaS-tRNA(Ile2)-ATP complex, C34 is trapped within a pocket far away from the ATP-binding site. In the agmatine-containing crystals, C34 is located near the AMPCPP γ-phosphate in the kinase module, demonstrating that agmatine is essential for placing C34 in the active site. These observations also provide the structural dynamics for agm(2)C formation.


    Organizational Affiliation

    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized proteinA440Archaeoglobus fulgidusMutation(s): 0 
Gene Names: AF_2259
EC: 6.3.4.22
UniProt
Find proteins for O28025 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O28025 
Go to UniProtKB:  O28025
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO28025
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (78-MER)B78Archaeoglobus fulgidus
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC

Download Ideal Coordinates CCD File 
C [auth A]DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
 Ligand Interaction
AG2
Query on AG2

Download Ideal Coordinates CCD File 
D [auth A]AGMATINE
C5 H14 N4
QYPPJABKJHAVHS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.789α = 90
b = 130.789β = 90
c = 87.087γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-12
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references