5IOS

Flavin-dependent thymidylate synthase R90A variant in complex with FAD and deoxyuridine monophosphate

• PDB DOI: https://doi.org/10.2210/pdb5IOS/pdb

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-03-08 Released: 2016-06-08 
• Deposition Author(s): Bernard, S.M., Stull, F.W., Smith, J.L.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.211 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Literature

Deprotonations in the Reaction of Flavin-Dependent Thymidylate Synthase.

Stull, F.W., Bernard, S.M., Sapra, A., Smith, J.L., Zuiderweg, E.R., Palfey, B.A.

(2016) Biochemistry 55: 3261-3269

• PubMed: 27214228 
• DOI: https://doi.org/10.1021/acs.biochem.6b00510
• Primary Citation of Related Structures:  
  5IOQ, 5IOR, 5IOS, 5IOT


• PubMed Abstract: 
  

  Many microorganisms use flavin-dependent thymidylate synthase (FDTS) to synthesize the essential nucleotide 2'-deoxythymidine 5'-monophosphate (dTMP) from 2'-deoxyuridine 5'-monophosphate (dUMP), 5,10-methylenetetrahydrofolate (CH2THF), and NADPH. FDTSs have a structure that is unrelated to the thymidylate synthase used by humans and a very different mechanism. Here we report nuclear magnetic resonance evidence that FDTS ionizes N3 of dUMP using an active-site arginine. The ionized form of dUMP is largely responsible for the changes in the flavin absorbance spectrum of FDTS upon dUMP binding. dUMP analogues also suggest that the phosphate of dUMP acts as the base that removes the proton from C5 of the dUMP-methylene intermediate in the FDTS-catalyzed reaction. These findings establish additional differences between the mechanisms of FDTS and human thymidylate synthase.

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Organizational Affiliation: 

Program in Chemical Biology, University of Michigan , Ann Arbor, Michigan 48109, United States.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 114.05 kDa 
• Atom Count: 7,588 
• Modelled Residue Count: 857 
• Deposited Residue Count: 928 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase ThyX	A, B, C, D	232	Thermotoga maritima MSB8	Mutation(s): 1  Gene Names: thyX, thy1, TM_0449 EC: 2.1.1.148
UniProt
Find proteins for Q9WYT0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYT0  Go to UniProtKB:  Q9WYT0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], H [auth B], I [auth C], K [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
UMP	F [auth A], G [auth A], J [auth C], L [auth D]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
UMP	Binding MOAD:  5IOS	Kd: 1.40e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.211 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.071	α = 90
b = 116.217	β = 90
c = 141.007	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-06-08 
Deposition Author(s): Bernard, S.M., Stull, F.W., Smith, J.L.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE 1213620
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01DK042303
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM081544

Revision History  

• Version 1.0: 2016-06-08
  Type: Initial release
  
• Version 1.1: 2016-06-22
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description