6gpe: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,097 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,097 edits
No edit summary
 
(One intermediate revision by the same user not shown)
Line 1: Line 1:


==Crystal Structure of the CsiD Glutarate Hydroxylase==
==Crystal Structure of the CsiD Glutarate Hydroxylase==
<StructureSection load='6gpe' size='340' side='right' caption='[[6gpe]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='6gpe' size='340' side='right'caption='[[6gpe]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6gpe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GPE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GPE FirstGlance]. <br>
<table><tr><td colspan='2'>[[6gpe]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GPE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6GPE FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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]] 2.2&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6gpe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gpe OCA], [http://pdbe.org/6gpe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gpe RCSB], [http://www.ebi.ac.uk/pdbsum/6gpe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gpe ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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=6gpe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gpe OCA], [https://pdbe.org/6gpe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6gpe RCSB], [https://www.ebi.ac.uk/pdbsum/6gpe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6gpe ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/CSID_ECOLI CSID_ECOLI]] May be involved in the control of utilization of gamma-aminobutyric acid.[HAMAP-Rule:MF_01083]
[https://www.uniprot.org/uniprot/GLAH_ECOLI GLAH_ECOLI] Acts as an alpha-ketoglutarate-dependent dioxygenase catalyzing hydroxylation of glutarate (GA) to L-2-hydroxyglutarate (L2HG) in the stationary phase of E.coli. Functions in a L-lysine degradation pathway that proceeds via cadaverine, glutarate and L-2-hydroxyglutarate. Other dicarboxylic acids (oxalate, malonate, succinate, adipate, and pimelate) are not substrates for this enzyme.<ref>PMID:30498244</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Lysine degradation has remained elusive in many organisms including Escherichia coli. Here we report catabolism of lysine to succinate in E. coli involving glutarate and L-2-hydroxyglutarate as intermediates. We show that CsiD acts as an alpha-ketoglutarate-dependent dioxygenase catalysing hydroxylation of glutarate to L-2-hydroxyglutarate. CsiD is found widespread in bacteria. We present crystal structures of CsiD in complex with glutarate, succinate, and the inhibitor N-oxalyl-glycine, demonstrating strong discrimination between the structurally related ligands. We show that L-2-hydroxyglutarate is converted to alpha-ketoglutarate by LhgO acting as a membrane-bound, ubiquinone-linked dehydrogenase. Lysine enters the pathway via 5-aminovalerate by the promiscuous enzymes GabT and GabD. We demonstrate that repression of the pathway by CsiR is relieved upon glutarate binding. In conclusion, lysine degradation provides an important link in central metabolism. Our results imply the gut microbiome as a potential source of glutarate and L-2-hydroxyglutarate associated with human diseases such as cancer and organic acidurias.
 
Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate.,Knorr S, Sinn M, Galetskiy D, Williams RM, Wang C, Muller N, Mayans O, Schleheck D, Hartig JS Nat Commun. 2018 Nov 29;9(1):5071. doi: 10.1038/s41467-018-07563-6. PMID:30498244<ref>PMID:30498244</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6gpe" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Hartig, J S]]
[[Category: Escherichia coli K-12]]
[[Category: Mayans, O]]
[[Category: Large Structures]]
[[Category: Williams, R M]]
[[Category: Hartig JS]]
[[Category: Alpha-ketoglutarate-dependent]]
[[Category: Mayans O]]
[[Category: Glutarate hydroxylase]]
[[Category: Williams RM]]
[[Category: Hydrolase]]
[[Category: Jelly roll]]

Latest revision as of 07:49, 7 February 2024

Crystal Structure of the CsiD Glutarate Hydroxylase

6gpe, resolution 2.20Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=6gpe&oldid=4045955"