4GTA

T. Maritima FDTS with FAD, dUMP, and Folinic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Folate binding site of flavin-dependent thymidylate synthase.

Koehn, E.M.Perissinotti, L.L.Moghram, S.Prabhakar, A.Lesley, S.A.Mathews, I.I.Kohen, A.

(2012) Proc.Natl.Acad.Sci.USA 109: 15722-15727

  • DOI: 10.1073/pnas.1206077109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The DNA nucleotide thymidylate is synthesized by the enzyme thymidylate synthase, which catalyzes the reductive methylation of deoxyuridylate using the cofactor methylene-tetrahydrofolate (CH(2)H(4)folate). Most organisms, including humans, rely on t ...

    The DNA nucleotide thymidylate is synthesized by the enzyme thymidylate synthase, which catalyzes the reductive methylation of deoxyuridylate using the cofactor methylene-tetrahydrofolate (CH(2)H(4)folate). Most organisms, including humans, rely on the thyA- or TYMS-encoded classic thymidylate synthase, whereas, certain microorganisms, including all Rickettsia and other pathogens, use an alternative thyX-encoded flavin-dependent thymidylate synthase (FDTS). Although several crystal structures of FDTSs have been reported, the absence of a structure with folates limits understanding of the molecular mechanism and the scope of drug design for these enzymes. Here we present X-ray crystal structures of FDTS with several folate derivatives, which together with mutagenesis, kinetic analysis, and computer modeling shed light on the cofactor binding and function. The unique structural data will likely facilitate further elucidation of FDTSs' mechanism and the design of structure-based inhibitors as potential leads to new antimicrobial drugs.


    Organizational Affiliation

    Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthase thyX
A
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FFO
Query on FFO

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A
N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid
[6S]-5-FORMYL-TETRAHYDROFOLATE; 6S-FOLINIC ACID
C20 H23 N7 O7
VVIAGPKUTFNRDU-STQMWFEESA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
UMP
Query on UMP

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Download CCD File 
A
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.164 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 110.300α = 90.00
b = 110.300β = 90.00
c = 121.030γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
Blu-Icedata collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-17
    Type: Initial release