Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.99 kDa 
• Atom Count: 2504 
• Residue Count: 298 
• Unique protein chains: 1

3VRH

Crystal structure of ph0300

• DOI: 10.2210/pdb3VRH/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-10 Released: 2013-03-13 
• Deposition Author(s): Nakagawa, H., Kuratani, M., Goto-Ito, S., Ito, T., Sekine, S.I., Yokoyama, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.244 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA.

Nakagawa, H., Kuratani, M., Goto-Ito, S., Ito, T., Katsura, K., Terada, T., Shirouzu, M., Sekine, S.I., Shigi, N., Yokoyama, S.

(2013) Proteins 

• PubMed: 23444054 
• DOI: 10.1002/prot.24273
• Primary Citation of Related Structures:  
  3VRH


• PubMed Abstract: 
  

In thermophilic bacteria, specific 2-thiolation occurs on the conserved ribothymidine at position 54 (T54) in tRNAs, which is necessary for survival at high temperatures. T54 2-thiolation is achieved by the tRNA thiouridine synthetase TtuA and sulfur-carrier proteins. TtuA has five conserved CXXC/H motifs and the signature PP motif, and belongs to the TtcA family of tRNA 2-thiolation enzymes, for which there is currently no structural information. In this study, we determined the crystal structure of a TtuA homolog from the hyperthermophilic archeon Pyrococcus horikoshii at 2.1 Å resolution. The P. horikoshii TtuA forms a homodimer, and each subunit contains a catalytic domain and unique N- and C-terminal zinc fingers. The catalytic domain has much higher structural similarity to that of another tRNA modification enzyme, TilS (tRNA(Ile)₂ lysidine synthetase), than to the other type of tRNA 2-thiolation enzyme, MnmA. Three conserved cysteine residues are clustered in the putative catalytic site, which is not present in TilS. An in vivo mutational analysis in the bacterium Thermus thermophilus demonstrated that the three conserved cysteine residues and the putative ATP-binding residues in the catalytic domain are important for the TtuA activity. A positively charged surface that includes the catalytic site and the two zinc fingers is likely to provide the tRNA-binding site.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein PH0300	A	310	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: PH0300, ttuA EC: 2.8.1
Find proteins for O58038 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58038  Go to UniProtKB:  O58038

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BCN	A	BICINE C6 H13 N O4 FSVCELGFZIQNCK-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.244 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.071	α = 90
b = 70.071	β = 90
c = 128.636	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-10 
• Released Date: 2013-03-13 
Deposition Author(s): Nakagawa, H., Kuratani, M., Goto-Ito, S., Ito, T., Sekine, S.I., Yokoyama, S.

Revision History 

• Version 1.0: 2013-03-13
  Type: Initial release