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The | ==Crystal structure of Pyruvic Oxime Dioxygenase (POD) from Alcaligenes faecalis deleted N-terminal 18 residues== | ||
<StructureSection load='8iqa' size='340' side='right'caption='[[8iqa]], [[Resolution|resolution]] 1.55Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8iqa]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_faecalis_subsp._faecalis_NBRC_13111 Alcaligenes faecalis subsp. faecalis NBRC 13111]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8IQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IQA 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]] 1.551Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=8iqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8iqa OCA], [https://pdbe.org/8iqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8iqa RCSB], [https://www.ebi.ac.uk/pdbsum/8iqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8iqa ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A0A2N3A3_ALCFA A0A0A2N3A3_ALCFA] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Nitrification by heterotrophic microorganisms is an important part of the nitrogen cycle in the environment. The enzyme responsible for the core function of heterotrophic nitrification is pyruvic oxime dioxygenase (POD). POD is a non-heme, Fe(II)-dependent enzyme that catalyzes the dioxygenation of pyruvic oxime to produce pyruvate and nitrite. To analyze the catalytic mechanism of POD, the crystal structure of POD from Alcaligenes faecalis (AfPOD) was determined at 1.76 A resolution. The enzyme is a homotetramer, and the subunit structure is homologous to those of class II aldolases, in particular, a zinc-dependent L-fuculose-1-phosphate aldolase. The active site of the subunit is located at the bottom of a cleft formed with an adjacent subunit. The iron ion at the active site is coordinated by three histidines and three water molecules in an octahedral geometry. The putative oxygen tunnel was connected between the active site and the central cavity of the tetramer. The N-terminal region of AfPOD, which is essential for catalytic activity, is disordered in the crystal. Structure prediction with AlphaFold2 combined with mutational experiments suggested that the disordered N-terminal region adopts an alpha-helix conformation and participates in the formation of the active site. The catalytic mechanism of the dioxygenase reaction by POD is discussed on the basis of the molecular docking model.IMPORTANCEOur knowledge of nitrification has increased considerably in recent decades with the discovery of new nitrifying microorganisms and the characterization of their biochemical processes. Some heterotrophic bacteria and fungi are known to show nitrification activities, but the molecular mechanisms have been poorly understood. Here, we performed a structural characterization of pyruvic oxime dioxygenase (POD), a key enzyme in heterotrophic nitrification that produces nitrite from ammonia using pyruvic oxime as an intermediate. Structural and enzymatic analyses revealed that POD is a unique dioxygenase with features such as an aldolase backbone, an N-terminal alpha-helix, and an oxygen tunnel. Our results provide insights not only into the molecular mechanisms but also into the design of specific inhibitors of heterotrophic nitrification. | |||
Structural characterization of pyruvic oxime dioxygenase, a key enzyme in heterotrophic nitrification.,Tsujino S, Yamada Y, Senda M, Nakamura A, Senda T, Fujiwara T J Bacteriol. 2025 Feb 20;207(2):e0034224. doi: 10.1128/jb.00342-24. Epub 2025 Jan , 8. PMID:39772954<ref>PMID:39772954</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 8iqa" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Alcaligenes faecalis subsp. faecalis NBRC 13111]] | |||
[[Category: Large Structures]] | |||
[[Category: Fujiwara T]] | |||
[[Category: Tsujino S]] | |||
[[Category: Yamada Y]] | |||