5c3p: Difference between revisions
New page: '''Unreleased structure''' The entry 5c3p is ON HOLD Authors: Li, W., Zhang, T., Ding, J. Description: Crystal Structure of a fungal enzyme in complex with the cofactor [[Category: Unr... |
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The | ==Crystal structure of the full-length Neurospora crassa T7H in complex with alpha-KG== | ||
<StructureSection load='5c3p' size='340' side='right'caption='[[5c3p]], [[Resolution|resolution]] 2.10Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5c3p]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Neurospora_crassa Neurospora crassa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C3P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C3P FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></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=5c3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c3p OCA], [https://pdbe.org/5c3p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c3p RCSB], [https://www.ebi.ac.uk/pdbsum/5c3p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c3p ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q7RYZ9_NEUCR Q7RYZ9_NEUCR] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
TET proteins play a vital role in active DNA demethylation in mammals and thus have important functions in many essential cellular processes. The chemistry for the conversion of 5mC to 5hmC, 5fC and 5caC catalysed by TET proteins is similar to that of T to 5hmU, 5fU and 5caU catalysed by thymine-7-hydroxylase (T7H) in the nucleotide anabolism in fungi. Here, we report the crystal structures and biochemical properties of Neurospora crassa T7H. T7H can bind the substrates only in the presence of cosubstrate, and binding of different substrates does not induce notable conformational changes. T7H exhibits comparable binding affinity for T and 5hmU, but 3-fold lower affinity for 5fU. Residues Phe292, Tyr217 and Arg190 play critical roles in substrate binding and catalysis, and the interactions of the C5 modification group of substrates with the cosubstrate and enzyme contribute to the slightly varied binding affinity and activity towards different substrates. After the catalysis, the products are released and new cosubstrate and substrate are reloaded to conduct the next oxidation reaction. Our data reveal the molecular basis for substrate specificity and catalytic mechanism of T7H and provide new insights into the molecular mechanism of substrate recognition and catalysis of TET proteins. | |||
Molecular basis for the substrate specificity and catalytic mechanism of thymine-7-hydroxylase in fungi.,Li W, Zhang T, Ding J Nucleic Acids Res. 2015 Oct 1. pii: gkv979. PMID:26429971<ref>PMID:26429971</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5c3p" style="background-color:#fffaf0;"></div> | ||
[[Category: Ding | |||
[[Category: Li | ==See Also== | ||
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Neurospora crassa]] | |||
[[Category: Ding J]] | |||
[[Category: Li W]] | |||
[[Category: Zhang T]] | |||
Latest revision as of 19:06, 8 November 2023
Crystal structure of the full-length Neurospora crassa T7H in complex with alpha-KGCrystal structure of the full-length Neurospora crassa T7H in complex with alpha-KG
Structural highlights
FunctionPublication Abstract from PubMedTET proteins play a vital role in active DNA demethylation in mammals and thus have important functions in many essential cellular processes. The chemistry for the conversion of 5mC to 5hmC, 5fC and 5caC catalysed by TET proteins is similar to that of T to 5hmU, 5fU and 5caU catalysed by thymine-7-hydroxylase (T7H) in the nucleotide anabolism in fungi. Here, we report the crystal structures and biochemical properties of Neurospora crassa T7H. T7H can bind the substrates only in the presence of cosubstrate, and binding of different substrates does not induce notable conformational changes. T7H exhibits comparable binding affinity for T and 5hmU, but 3-fold lower affinity for 5fU. Residues Phe292, Tyr217 and Arg190 play critical roles in substrate binding and catalysis, and the interactions of the C5 modification group of substrates with the cosubstrate and enzyme contribute to the slightly varied binding affinity and activity towards different substrates. After the catalysis, the products are released and new cosubstrate and substrate are reloaded to conduct the next oxidation reaction. Our data reveal the molecular basis for substrate specificity and catalytic mechanism of T7H and provide new insights into the molecular mechanism of substrate recognition and catalysis of TET proteins. Molecular basis for the substrate specificity and catalytic mechanism of thymine-7-hydroxylase in fungi.,Li W, Zhang T, Ding J Nucleic Acids Res. 2015 Oct 1. pii: gkv979. PMID:26429971[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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