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6nnr

From Proteopedia

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Current revision

high-resolution structure of wild-type E. coli thymidylate synthase

Structural highlights

6nnr is a 2 chain structure with sequence from Escherichia coli K-12. This structure supersedes the now removed PDB entries 4knz, 4iw5 and 2g8o. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.05Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TYSY_ECOLI Provides the sole de novo source of dTMP for DNA biosynthesis. This protein also binds to its mRNA thus repressing its own translation.

Publication Abstract from PubMed

Thymidylate synthase (TSase) produces the sole intracellular de novo source of thymidine (i.e. the DNA base T) and thus is a common target for antibiotic and anticancer drugs. Mg2+ has been reported to affect TSase activity, but the mechanism of this interaction has not been investigated. Here we show that Mg2+ binds to the surface of Escherichia coli TSase and affects the kinetics of hydride transfer at the interior active site (16 A away). Examination of the crystal structures identifies a Mg2+ near the glutamyl moiety of the folate cofactor, providing the first structural evidence for Mg2+ binding to TSase. The kinetics and NMR relaxation experiments suggest that the weak binding of Mg2+ to the protein surface stabilizes the closed conformation of the ternary enzyme complex and reduces the entropy of activation on the hydride transfer step. Mg2+ accelerates the hydride transfer by ca. 7-fold but does not affect the magnitude or temperature-dependence of the intrinsic kinetic isotope effect. These results suggest that Mg2+ facilitates the protein motions that bring the hydride donor and acceptor together, but it does not change the tunneling ready state of the hydride transfer. These findings highlight how variations in cellular Mg2+ concentration can modulate enzyme activity through long-range interactions in the protein, rather than binding at the active site. The interaction of Mg2+ with the glutamyl-tail of the folate cofactor and nonconserved residues of bacterial TSase may assist in designing antifolates with poly-glutamyl substitutes as species-specific antibiotic drugs.

Mg2+ binds to the surface of thymidylate synthase and affects hydride transfer at the interior active site.,Wang Z, Sapienza PJ, Abeysinghe T, Luzum C, Lee AL, Finer-Moore JS, Stroud RM, Kohen A J Am Chem Soc. 2013 Apr 23. PMID:23611499^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wang Z, Sapienza PJ, Abeysinghe T, Luzum C, Lee AL, Finer-Moore JS, Stroud RM, Kohen A. Mg2+ binds to the surface of thymidylate synthase and affects hydride transfer at the interior active site. J Am Chem Soc. 2013 Apr 23. PMID:23611499 doi:10.1021/ja400761x

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6nnr"

Categories: Escherichia coli K-12 | Large Structures | Finer-Moore J | Stroud RM

@@ Line 1: / Line 1: @@
 ==high-resolution structure of wild-type E. coli thymidylate synthase==
-<StructureSection load='6nnr' size='340' side='right' caption='[[6nnr]], [[Resolution|resolution]] 1.05&Aring;' scene=''>
+<StructureSection load='6nnr' size='340' side='right'caption='[[6nnr]], [[Resolution|resolution]] 1.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6nnr]] is a 2 chain structure. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4knz 4knz], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4iw5 4iw5] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g8o 2g8o]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NNR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NNR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6nnr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4knz 4knz], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4iw5 4iw5] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g8o 2g8o]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NNR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NNR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CB3:10-PROPARGYL-5,8-DIDEAZAFOLIC+ACID'>CB3</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=UMC:2-DEOXY-5-URIDYLIC+ACID'>UMC</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.05&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CB3:10-PROPARGYL-5,8-DIDEAZAFOLIC+ACID'>CB3</scene>, <scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=UMC:2-DEOXY-5-URIDYLIC+ACID'>UMC</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidylate_synthase Thymidylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.45 2.1.1.45] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6nnr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nnr OCA], [https://pdbe.org/6nnr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nnr RCSB], [https://www.ebi.ac.uk/pdbsum/6nnr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nnr ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6nnr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nnr OCA], [http://pdbe.org/6nnr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nnr RCSB], [http://www.ebi.ac.uk/pdbsum/6nnr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nnr ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TYSY_ECOLI TYSY_ECOLI]] Provides the sole de novo source of dTMP for DNA biosynthesis. This protein also binds to its mRNA thus repressing its own translation.
+[https://www.uniprot.org/uniprot/TYSY_ECOLI TYSY_ECOLI] Provides the sole de novo source of dTMP for DNA biosynthesis. This protein also binds to its mRNA thus repressing its own translation.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 19: @@
 </div>
 <div class="pdbe-citations 6nnr" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Thymidylate synthase 3D structures|Thymidylate synthase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Thymidylate synthase]]
+[[Category: Escherichia coli K-12]]
-[[Category: Finer-Moore, J]]
+[[Category: Large Structures]]
-[[Category: Stroud, R M]]
+[[Category: Finer-Moore J]]
-[[Category: Cancer drug target]]
+[[Category: Stroud RM]]
-[[Category: Hydride transfer]]
-[[Category: Methyl transfer]]
-[[Category: Nucleotide synthesis]]
-[[Category: Transferase]]

6nnr

From Proteopedia

Current revision

high-resolution structure of wild-type E. coli thymidylate synthase

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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