5XOX

Crystal structure of tRNA(His) guanylyltranserase from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of tRNA(His) guanylyltransferase from Saccharomyces cerevisiae

Lee, K.Lee, E.H.Son, J.Hwang, K.Y.

(2017) Biochem Biophys Res Commun 490: 400-405

  • DOI: https://doi.org/10.1016/j.bbrc.2017.06.054
  • Primary Citation of Related Structures:  
    5XOX

  • PubMed Abstract: 

    tRNA maturation involves several steps, including processing, splicing, CCA addition, and posttranscriptional modifications. tRNA His guanylyltransferase (Thg1) is the only enzyme known to catalyze templated nucleotide addition in the 3'-5' direction, unlike other DNA and RNA polymerases. For a better understanding of its unique catalytic mechanism at the molecular level, we determined the crystal structure of GTP-bound Thg1 from Saccharomyces cerevisiae at the maximum resolution of 3.0 Å. The structure revealed the enzyme to have a tetrameric conformation that is well conserved among different species, and the GTP molecule was clearly bound at the active site, coordinating with two magnesium ions. In addition, two flexible protomers at the potential binding site (PBS) for tRNA His were observed. We suggest that the PBS of the tetramer could also be one of the sites for interaction with partner proteins.


  • Organizational Affiliation

    Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-791, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA(His) guanylyltransferase
A, B, C, D, E
A, B, C, D, E, F
243Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: THG1YGR024C
EC: 2.7.7.79
UniProt
Find proteins for P53215 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53215 
Go to UniProtKB:  P53215
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53215
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
O [auth C],
T [auth D],
W [auth E]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
J [auth A],
K [auth B],
R [auth C],
S [auth D],
Z [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
M [auth B]
N [auth B]
P [auth C]
H [auth A],
I [auth A],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
U [auth D],
V [auth D],
X [auth E],
Y [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.703α = 90
b = 164.703β = 90
c = 275.891γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation of KoreaKorea, Republic Of2017R1A2B2005666

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description