3W3S

Crystal structure of A. aeolicus tRNASec in complex with M. kandleri SerRS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.095 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Tertiary structure of bacterial selenocysteine tRNA

Itoh, Y.Sekine, S.Suetsugu, S.Yokoyama, S.

(2013) Nucleic Acids Res. 41: 6729-6738

  • DOI: 10.1093/nar/gkt321

  • PubMed Abstract: 
  • Selenocysteine (Sec) is translationally incorporated into proteins in response to the UGA codon. The tRNA specific to Sec (tRNA(Sec)) is first ligated with serine by seryl-tRNA synthetase (SerRS). In the present study, we determined the 3.1 Å crystal ...

    Selenocysteine (Sec) is translationally incorporated into proteins in response to the UGA codon. The tRNA specific to Sec (tRNA(Sec)) is first ligated with serine by seryl-tRNA synthetase (SerRS). In the present study, we determined the 3.1 Å crystal structure of the tRNA(Sec) from the bacterium Aquifex aeolicus, in complex with the heterologous SerRS from the archaeon Methanopyrus kandleri. The bacterial tRNA(Sec) assumes the L-shaped structure, from which the long extra arm protrudes. Although the D-arm conformation and the extra-arm orientation are similar to those of eukaryal/archaeal tRNA(Sec)s, A. aeolicus tRNA(Sec) has unique base triples, G14:C21:U8 and C15:G20a:G48, which occupy the positions corresponding to the U8:A14 and R15:Y48 tertiary base pairs of canonical tRNAs. Methanopyrus kandleri SerRS exhibited serine ligation activity toward A. aeolicus tRNA(Sec) in vitro. The SerRS N-terminal domain interacts with the extra-arm stem and the outer corner of tRNA(Sec). Similar interactions exist in the reported tRNA(Ser) and SerRS complex structure from the bacterium Thermus thermophilus. Although the catalytic C-terminal domain of M. kandleri SerRS lacks interactions with A. aeolicus tRNA(Sec) in the present complex structure, the conformational flexibility of SerRS is likely to allow the CCA terminal region of tRNA(Sec) to enter the SerRS catalytic site.


    Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type-2 serine--tRNA ligase
A
527Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)Mutation(s): 11 
Gene Names: serS
EC: 6.1.1.11
Find proteins for Q8TVD2 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938))
Go to UniProtKB:  Q8TVD2
Entity ID: 2
MoleculeChainsLengthOrganism
selenocysteine tRNAB99Aquifex aeolicus VF5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PT
Query on PT

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Download CCD File 
A
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
 Ligand Interaction
SSA
Query on SSA

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Download CCD File 
A
5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
C13 H19 N7 O8 S
HQXFJGONGJPTLZ-YTMOPEAISA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.095 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.204 
  • Space Group: I 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 272.817α = 90.00
b = 272.817β = 90.00
c = 272.817γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
ADSCdata collection
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-05-22
    Type: Database references
  • Version 1.2: 2013-08-07
    Type: Database references