6J61

Crystal Structure of Thymidylate Synthase, Thy1, from Thermus thermophilus having an Extra C Terminal Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the flavin-dependent thymidylate synthase Thy1 from Thermus thermophilus with an extra C-terminal domain.

Ogawa, A.Sampei, G.Kawai, G.

(2019) Acta Crystallogr F Struct Biol Commun 75: 450-454

  • DOI: https://doi.org/10.1107/S2053230X19007192
  • Primary Citation of Related Structures:  
    6J61

  • PubMed Abstract: 

    The thymidylate synthases ThyA and Thy1 are enzymes that catalyse the formation of thymidine monophosphate from 2'-deoxyuridine monophosphate. Thy1 (or ThyX) requires flavin for catalytic reactions, while ThyA does not. In the present study, the crystal structure of the flavin-dependent thymidylate synthase Thy1 from Thermus thermophilus HB8 (TtThy1, TTHA1096) was determined in complex with FAD and phosphate at 2.5 Å resolution. TtThy1 is a tetrameric molecule like other Thy1 proteins, to which four FAD molecules are bound. In the crystal of TtThy1, two phosphate ions were bound to each dUMP-binding site. The characteristic feature of TtThy1 is the existence of an extra C-terminal domain (CTD) consisting of three α-helices and a β-strand. The function of the CTD is unknown and database analysis showed that this CTD is only shared by part of the Deinococcus-Thermus phylum.


  • Organizational Affiliation

    Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Narashino, Chiba 275-0016, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flavin-dependent thymidylate synthase
A, B, C, D
270Thermus thermophilus HB8Mutation(s): 0 
Gene Names: thyXTTHA1096
EC: 2.1.1.148
UniProt
Find proteins for Q5SJB8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJB8 
Go to UniProtKB:  Q5SJB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SJB8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
K [auth C],
N [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth B]
I [auth B]
L [auth C]
F [auth A],
G [auth A],
H [auth B],
I [auth B],
L [auth C],
M [auth C],
O [auth D],
P [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.027α = 90
b = 68.362β = 115.12
c = 134.083γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description