View source for 6qkb


==Crystal structure of the beta-hydroxyaspartate aldolase of Paracoccus denitrificans==
<StructureSection load='6qkb' size='340' side='right'caption='[[6qkb]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6qkb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QKB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QKB 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]] 1.701&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=6qkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qkb OCA], [https://pdbe.org/6qkb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qkb RCSB], [https://www.ebi.ac.uk/pdbsum/6qkb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qkb ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/BHCC_PARDP BHCC_PARDP] Catalyzes the condensation of glyoxylate and glycine into (2R,3S)-beta-hydroxyaspartate ((3S)-3-hydroxy-D-aspartate). Is essential for the growth of P.denitrificans in the presence of glycolate and glyoxylate since it functions in glyoxylate assimilation via the beta-hydroxyaspartate cycle (BHAC). Is also able to catalyze the reverse reaction in vitro, i.e. the cleavage of (3S)-3-hydroxy-D-aspartate, and that of D-threonine to a lesser extent.<ref>PMID:31723261</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
One of the most abundant sources of organic carbon in the ocean is glycolate, the secretion of which by marine phytoplankton results in an estimated annual flux of one petagram of glycolate in marine environments(1). Although it is generally accepted that glycolate is oxidized to glyoxylate by marine bacteria(2-4), the further fate of this C2 metabolite is not well understood. Here we show that ubiquitous marine Proteobacteria are able to assimilate glyoxylate via the beta-hydroxyaspartate cycle (BHAC) that was originally proposed 56 years ago(5). We elucidate the biochemistry of the BHAC and describe the structure of its key enzymes, including a previously unknown primary imine reductase. Overall, the BHAC enables the direct production of oxaloacetate from glyoxylate through only four enzymatic steps, representing-to our knowledge-the most efficient glyoxylate assimilation route described to date. Analysis of marine metagenomes shows that the BHAC is globally distributed and on average 20-fold more abundant than the glycerate pathway, the only other known pathway for net glyoxylate assimilation. In a field study of a phytoplankton bloom, we show that glycolate is present in high nanomolar concentrations and taken up by prokaryotes at rates that allow a full turnover of the glycolate pool within one week. During the bloom, genes that encode BHAC key enzymes are present in up to 1.5% of the bacterial community and actively transcribed, supporting the role of the BHAC in glycolate assimilation and suggesting a previously undescribed trophic interaction between autotrophic phytoplankton and heterotrophic bacterioplankton.

Marine Proteobacteria metabolize glycolate via the beta-hydroxyaspartate cycle.,Schada von Borzyskowski L, Severi F, Kruger K, Hermann L, Gilardet A, Sippel F, Pommerenke B, Claus P, Cortina NS, Glatter T, Zauner S, Zarzycki J, Fuchs BM, Bremer E, Maier UG, Amann RI, Erb TJ Nature. 2019 Nov;575(7783):500-504. doi: 10.1038/s41586-019-1748-4. Epub 2019 Nov, 13. PMID:31723261<ref>PMID:31723261</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6qkb" style="background-color:#fffaf0;"></div>

==See Also==
*[[Aldolase 3D structures|Aldolase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Paracoccus denitrificans]]
[[Category: Erb TJ]]
[[Category: Gilardet A]]
[[Category: Schada von Borzyskowski L]]
[[Category: Zarzycki J]]