1O28

Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga maritima with FdUMP at 2.1 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Functional Analysis of Substrate and Cofactor Complex Structures of a Thymidylate Synthase-Complementing Protein

Mathews, I.I.Deacon, A.M.Canaves, J.M.McMullan, D.Lesley, S.A.Agarwalla, S.Kuhn, P.

(2003) Structure 11: 677-690

  • Primary Citation of Related Structures:  
  • Also Cited By: 3N0C, 3N0B, 3G4A

  • PubMed Abstract: 
  • Like thymidylate synthase (TS) in eukaryotes, the thymidylate synthase-complementing proteins (TSCPs) are mandatory for cell survival of many prokaryotes in the absence of external sources of thymidylate. Details of the mechanism of this novel family ...

    Like thymidylate synthase (TS) in eukaryotes, the thymidylate synthase-complementing proteins (TSCPs) are mandatory for cell survival of many prokaryotes in the absence of external sources of thymidylate. Details of the mechanism of this novel family of enzymes are unknown. Here, we report the structural and functional analysis of a TSCP from Thermotoga maritima and its complexes with substrate, analogs, and cofactor. The structures presented here provide a basis for rationalizing the TSCP catalysis and reveal the possibility of the design of an inhibitor. We have identified a new helix-loop-strand FAD binding motif characteristic of the enzymes in the TSCP family. The presence of a hydrophobic core with residues conserved among the TSCP family suggests a common overall fold.


    Organizational Affiliation

    Stanford Synchrotron Radiation Laboratory, Stanford University, 2575 Sand Hill Road, SSRL MS 69, Menlo Park, CA 94025, USA. iimathew@stanford.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthase thyX
A, B, C, D
232Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Gene Names: thyX (thy1)
EC: 2.1.1.148
Find proteins for Q9WYT0 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9WYT0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A, B, C, D
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
UFP
Query on UFP

Download SDF File 
Download CCD File 
A, B, C, D
5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
C9 H12 F N2 O8 P
HFEKDTCAMMOLQP-RRKCRQDMSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
B, C, D
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.390α = 90.00
b = 116.709β = 90.00
c = 141.003γ = 90.00
Software Package:
Software NamePurpose
RESOLVEmodel building
RESOLVEphasing
CCP4data scaling
SCALAdata scaling
SOLVEphasing
CNSrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-24
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description
  • Version 1.4: 2018-07-18
    Type: Data collection, Database references