7jxf: Difference between revisions

Latest revision as of 06:26, 21 November 2024

E. coli TSase complex with a bi-substrate reaction intermediate diastereomer analog

Structural highlights

Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:	5HU, CXM, NA, VMV, VNM
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Methylation of 2-deoxyuridine-5'-monophosphate (dUMP) at the C5 position by the obligate dimeric thymidylate synthase (TSase) in the sole de novo biosynthetic pathway to thymidine 5'-monophosphate (dTMP) proceeds by forming a covalent ternary complex with dUMP and cosubstrate 5,10-methylenetetrahydrofolate. The crystal structure of an analog of this intermediate gives important mechanistic insights but does not explain the half-of-the-sites activity of the enzyme. Recent experiments showed that the C5 proton and the catalytic Cys are eliminated in a concerted manner from the covalent ternary complex to produce a noncovalent bisubstrate intermediate. Here, we report the crystal structure of TSase with a close synthetic analog of this intermediate in which it has partially reacted with the enzyme but in only one protomer, consistent with the half-of-the-sites activity of this enzyme. Quantum mechanics/molecular mechanics simulations confirmed that the analog could undergo catalysis. The crystal structure shows a new water 2.9 A from the critical C5 of the dUMP moiety, which in conjunction with other residues in the network, may be the elusive general base that abstracts the C5 proton of dUMP during the reaction.

Caught in Action: X-ray Structure of Thymidylate Synthase with Noncovalent Intermediate Analog.,Kholodar SA, Finer-Moore JS, Swiderek K, Arafet K, Moliner V, Stroud RM, Kohen A Biochemistry. 2021 Apr 8. doi: 10.1021/acs.biochem.1c00063. PMID:33829766^[1]

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

References

↑ Kholodar SA, Finer-Moore JS, Swiderek K, Arafet K, Moliner V, Stroud RM, Kohen A. Caught in Action: X-ray Structure of Thymidylate Synthase with Noncovalent Intermediate Analog. Biochemistry. 2021 Apr 8. doi: 10.1021/acs.biochem.1c00063. PMID:33829766 doi:https://dx.doi.org/10.1021/acs.biochem.1c00063

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OCA

[1] Kholodar SA, Finer-Moore JS, Swiderek K, Arafet K, Moliner V, Stroud RM, Kohen A. Caught in Action: X-ray Structure of Thymidylate Synthase with Noncovalent Intermediate Analog. Biochemistry. 2021 Apr 8. doi: 10.1021/acs.biochem.1c00063. PMID:33829766 doi:https://dx.doi.org/10.1021/acs.biochem.1c00063

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='7jxf' size='340' side='right'caption='[[7jxf]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7jxf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JXF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JXF FirstGlance]. <br>
+<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JXF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JXF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5HU:5-HYDROXYMETHYLURIDINE-2-DEOXY-5-MONOPHOSPHATE'>5HU</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=VMV:N-[4-({[(6S)-2,4-diamino-5,6,7,8-tetrahydropyrido[3,2-d]pyrimidin-6-yl]methyl}amino)benzene-1-carbonyl]-L-glutamic+acid'>VMV</scene>, <scene name='pdbligand=VNM:(2S)-2-({4-[({(6S)-2,4-diamino-5-[(1-{(2R,4S,5R)-4-hydroxy-5-[(phosphonooxy)methyl]tetrahydrofuran-2-yl}-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)methyl]-5,6,7,8-tetrahydropyrido[3,2-d]pyrimidin-6-yl}methyl)amino]benzoyl}amino)pentanedioic+acid+(non-preferred+name)'>VNM</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]] 1.5&#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=5HU:5-HYDROXYMETHYLURIDINE-2-DEOXY-5-MONOPHOSPHATE'>5HU</scene>, <scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=VMV:N-[4-({[(6S)-2,4-diamino-5,6,7,8-tetrahydropyrido[3,2-d]pyrimidin-6-yl]methyl}amino)benzene-1-carbonyl]-L-glutamic+acid'>VMV</scene>, <scene name='pdbligand=VNM:(2S)-2-({4-[({(6S)-2,4-diamino-5-[(1-{(2R,4S,5R)-4-hydroxy-5-[(phosphonooxy)methyl]tetrahydrofuran-2-yl}-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)methyl]-5,6,7,8-tetrahydropyrido[3,2-d]pyrimidin-6-yl}methyl)amino]benzoyl}amino)pentanedioic+acid+(non-preferred+name)'>VNM</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Thymidylate_synthase Thymidylate synthase], with EC number [https://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=7jxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jxf OCA], [https://pdbe.org/7jxf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jxf RCSB], [https://www.ebi.ac.uk/pdbsum/7jxf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jxf ProSAT]</span></td></tr>
 </table>
-== Function ==
-[[https://www.uniprot.org/uniprot/A0A029ILG4_ECOLX A0A029ILG4_ECOLX]] Catalyzes the reductive methylation of 2'-deoxyuridine-5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor and reductant in the reaction, yielding dihydrofolate (DHF) as a by-product. This enzymatic reaction provides an intracellular de novo source of dTMP, an essential precursor for DNA biosynthesis.[HAMAP-Rule:MF_00008]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 17: @@
 </div>
 <div class="pdbe-citations 7jxf" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Thymidylate synthase 3D structures|Thymidylate synthase 3D structures]]
 == References ==
 <references/>
@@ Line 25: / Line 25: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Thymidylate synthase]]
+[[Category: Finer-Moore J]]
-[[Category: Finer-Moore, J]]
+[[Category: Kholodar SA]]
-[[Category: Kholodar, S A]]
+[[Category: Kohen A]]
-[[Category: Kohen, A]]
+[[Category: Moliner V]]
-[[Category: Moliner, V]]
+[[Category: Stroud RM]]
-[[Category: Stroud, R M]]
+[[Category: Swiderek K]]
-[[Category: Swiderek, K]]
-[[Category: Biosynthetic protein]]
-[[Category: Half-sites activity]]
-[[Category: Inhibitor]]
-[[Category: Non covalent intermediate]]
-[[Category: Tmp synthesis]]

7jxf: Difference between revisions

Latest revision as of 06:26, 21 November 2024

E. coli TSase complex with a bi-substrate reaction intermediate diastereomer analog

Structural highlights

Publication Abstract from PubMed

See Also

References

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