5IOS | pdb_00005ios

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.211 (Depositor), 0.218 (DCC)
R-Value Work:
0.178 (Depositor), 0.187 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.biochem.6b00510
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WYT0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], H [auth B], I [auth C], K [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D]
UMP Query on UMP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], G [auth A], J [auth C], L [auth D]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.211 (Depositor), 0.218 (DCC)
R-Value Work: 0.178 (Depositor), 0.187 (DCC)
R-Value Observed: 0.180 (Depositor)

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

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-06-08

Deposition Author(s):

Bernard, S.M.

Stull, F.W.

Smith, J.L.

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 (Full details and data files)

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