1O28

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

PDB DOI: https://doi.org/10.2210/pdb1O28/pdb

Classification: TRANSFERASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-02-18 Released: 2003-06-24
Deposition Author(s): Mathews, I.I., Deacon, A.M., Canaves, J.M., McMullan, D., Lesley, S.A., Agarwalla, S., Kuhn, P., Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.240
R-Value Work: 0.193

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 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

PubMed: 12791256 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(03)00097-2
Primary Citation of Related Structures:
1O24, 1O25, 1O26, 1O27, 1O28, 1O29, 1O2A, 1O2B

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 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. [email protected]

Macromolecule Content

Total Structure Weight: 112.87 kDa
Atom Count: 7,770
Modelled Residue Count: 868
Deposited Residue Count: 928
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase thyX	A, B, C, D	232	Thermotoga maritima	Mutation(s): 0 Gene Names: TM0449 EC: 2.1.1 (PDB Primary Data), 2.1.1.148 (UniProt)
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WYT0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UFP Query on UFP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], G [auth B], K [auth C], N [auth D]	5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE C₉ H₁₂ F N₂ O₈ P HFEKDTCAMMOLQP-RRKCRQDMSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain N [auth D]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D]	F [auth A], H [auth B], J [auth C], M [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain L [auth C]	I [auth B], L [auth C], O [auth D], P [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D]