5XOX

Crystal structure of tRNA(His) guanylyltranserase from Saccharomyces cerevisiae

PDB DOI: https://doi.org/10.2210/pdb5XOX/pdb

Classification: TRANSFERASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-05-31 Released: 2017-07-12
Deposition Author(s): Lee, K., Lee, E.H., Son, J., Hwang, K.Y.
Funding Organization(s): National Research Foundation of Korea

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.274 (Depositor), 0.270 (DCC)
R-Value Work:
0.239 (Depositor), 0.240 (DCC)
R-Value Observed:
0.240 (Depositor)

Starting Model: experimental
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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

PubMed: 28623126 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 175.06 kDa
Atom Count: 10,372
Modelled Residue Count: 1,225
Deposited Residue Count: 1,458
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA(His) guanylyltransferase	A, B, C, D, E A, B, C, D, E, F	243	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: THG1, YGR024C 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53215
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain T [auth D] SDF format, chain W [auth E] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E]	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		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain T [auth D] Focus chain W [auth E] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain T [auth D] Focus chain W [auth E]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain R [auth C] SDF format, chain S [auth D] SDF format, chain Z [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth D] mmCIF format, chain Z [auth E]	J [auth A], K [auth B], R [auth C], S [auth D], Z [auth E]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain Z [auth E] Interactions & Density Focus chain J [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain Z [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain X [auth E] SDF format, chain Y [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E]	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		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth E] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.274 (Depositor), 0.270 (DCC)
R-Value Work: 0.239 (Depositor), 0.240 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.703	α = 90
b = 164.703	β = 90
c = 275.891	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-07-12

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation of Korea	Korea, Republic Of	2017R1A2B2005666

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