7w5t: Difference between revisions
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==A nonheme iron- and alpha-ketoglutarate- dependent halogenase that catalyzes nucleotide substrates== | ==A nonheme iron- and alpha-ketoglutarate- dependent halogenase that catalyzes nucleotide substrates== | ||
<StructureSection load='7w5t' size='340' side='right'caption='[[7w5t]]' scene=''> | <StructureSection load='7w5t' size='340' side='right'caption='[[7w5t]], [[Resolution|resolution]] 1.74Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W5T FirstGlance]. <br> | <table><tr><td colspan='2'>[[7w5t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinomadura_sp._ATCC_39365 Actinomadura sp. ATCC 39365]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W5T FirstGlance]. <br> | ||
</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=7w5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w5t OCA], [https://pdbe.org/7w5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w5t RCSB], [https://www.ebi.ac.uk/pdbsum/7w5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w5t ProSAT]</span></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]] 1.74Å</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7w5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w5t OCA], [https://pdbe.org/7w5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w5t RCSB], [https://www.ebi.ac.uk/pdbsum/7w5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w5t ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A1U8X168_9ACTN A0A1U8X168_9ACTN] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Nonheme iron- and alpha-ketoglutarate (alphaKG)-dependent halogenases (NHFeHals), which catalyze the regio- and stereoselective halogenation of the unactivated C(sp(3))-H bonds, exhibit tremendous potential in the challenging asymmetric halogenation. AdeV from Actinomadura sp. ATCC 39365 is the first identified carrier protein-free NHFeHal that catalyzes the chlorination of nucleotide 2'-deoxyadenosine-5'-monophosphate (2'-dAMP) to afford 2'-chloro-2'-deoxyadenosine-5'-monophosphate. Here, we determined the complex crystal structures of AdeV/Fe(II)/Cl and AdeV/Fe(II)/Cl/alphaKG at resolutions of 1.76 and 1.74 A, respectively. AdeV possesses a typical beta-sandwich topology with H194, H252, alphaKG, chloride, and one water molecule coordinating Fe(II) in the active site. Molecular docking, mutagenesis, and biochemical analyses reveal that the hydrophobic interactions and hydrogen bond network between the substrate-binding pocket and the adenine, deoxyribose, and phosphate moieties of 2'-dAMP are essential for substrate recognition. Residues H111, R177, and H192 might play important roles in the second-sphere interactions that control reaction partitioning. This study provides valuable insights into the catalytic selectivity of AdeV and will facilitate the rational engineering of AdeV and other NHFeHals for synthesis of halogenated nucleotides. IMPORTANCE Halogenated nucleotides are a group of important antibiotics and are clinically used as antiviral and anticancer drugs. AdeV is the first carrier protein-independent nonheme iron- and alpha-ketoglutarate (alphaKG)-dependent halogenase (NHFeHal) that can selectively halogenate nucleotides and exhibits restricted substrate specificity toward several 2'-dAMP analogues. Here, we determined the complex crystal structures of AdeV/Fe(II)/Cl and AdeV/Fe(II)/Cl/alphaKG. Molecular docking, mutagenesis, and biochemical analyses provide important insights into the catalytic selectivity of AdeV. This study will facilitate the rational engineering of AdeV and other carrier protein-independent NHFeHals for synthesis of halogenated nucleotides. | |||
Structural and Functional Insights into a Nonheme Iron- and alpha-Ketoglutarate-Dependent Halogenase That Catalyzes Chlorination of Nucleotide Substrates.,Dai L, Zhang X, Hu Y, Shen J, Zhang Q, Zhang L, Min J, Chen CC, Liu Y, Huang JW, Guo RT Appl Environ Microbiol. 2022 Apr 18:e0249721. doi: 10.1128/aem.02497-21. PMID:35435717<ref>PMID:35435717</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7w5t" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Actinomadura sp. ATCC 39365]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Chen CC]] | [[Category: Chen CC]] | ||
Latest revision as of 20:36, 29 November 2023
A nonheme iron- and alpha-ketoglutarate- dependent halogenase that catalyzes nucleotide substratesA nonheme iron- and alpha-ketoglutarate- dependent halogenase that catalyzes nucleotide substrates
Structural highlights
FunctionPublication Abstract from PubMedNonheme iron- and alpha-ketoglutarate (alphaKG)-dependent halogenases (NHFeHals), which catalyze the regio- and stereoselective halogenation of the unactivated C(sp(3))-H bonds, exhibit tremendous potential in the challenging asymmetric halogenation. AdeV from Actinomadura sp. ATCC 39365 is the first identified carrier protein-free NHFeHal that catalyzes the chlorination of nucleotide 2'-deoxyadenosine-5'-monophosphate (2'-dAMP) to afford 2'-chloro-2'-deoxyadenosine-5'-monophosphate. Here, we determined the complex crystal structures of AdeV/Fe(II)/Cl and AdeV/Fe(II)/Cl/alphaKG at resolutions of 1.76 and 1.74 A, respectively. AdeV possesses a typical beta-sandwich topology with H194, H252, alphaKG, chloride, and one water molecule coordinating Fe(II) in the active site. Molecular docking, mutagenesis, and biochemical analyses reveal that the hydrophobic interactions and hydrogen bond network between the substrate-binding pocket and the adenine, deoxyribose, and phosphate moieties of 2'-dAMP are essential for substrate recognition. Residues H111, R177, and H192 might play important roles in the second-sphere interactions that control reaction partitioning. This study provides valuable insights into the catalytic selectivity of AdeV and will facilitate the rational engineering of AdeV and other NHFeHals for synthesis of halogenated nucleotides. IMPORTANCE Halogenated nucleotides are a group of important antibiotics and are clinically used as antiviral and anticancer drugs. AdeV is the first carrier protein-independent nonheme iron- and alpha-ketoglutarate (alphaKG)-dependent halogenase (NHFeHal) that can selectively halogenate nucleotides and exhibits restricted substrate specificity toward several 2'-dAMP analogues. Here, we determined the complex crystal structures of AdeV/Fe(II)/Cl and AdeV/Fe(II)/Cl/alphaKG. Molecular docking, mutagenesis, and biochemical analyses provide important insights into the catalytic selectivity of AdeV. This study will facilitate the rational engineering of AdeV and other carrier protein-independent NHFeHals for synthesis of halogenated nucleotides. Structural and Functional Insights into a Nonheme Iron- and alpha-Ketoglutarate-Dependent Halogenase That Catalyzes Chlorination of Nucleotide Substrates.,Dai L, Zhang X, Hu Y, Shen J, Zhang Q, Zhang L, Min J, Chen CC, Liu Y, Huang JW, Guo RT Appl Environ Microbiol. 2022 Apr 18:e0249721. doi: 10.1128/aem.02497-21. PMID:35435717[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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