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6gpe

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Revision as of 06:53, 8 February 2023

Crystal Structure of the CsiD Glutarate Hydroxylase

Structural highlights

6gpe is a 2 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1]

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Knorr S, Sinn M, Galetskiy D, Williams RM, Wang C, Muller N, Mayans O, Schleheck D, Hartig JS. Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate. Nat Commun. 2018 Nov 29;9(1):5071. doi: 10.1038/s41467-018-07563-6. PMID:30498244 doi:http://dx.doi.org/10.1038/s41467-018-07563-6
↑ Knorr S, Sinn M, Galetskiy D, Williams RM, Wang C, Muller N, Mayans O, Schleheck D, Hartig JS. Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate. Nat Commun. 2018 Nov 29;9(1):5071. doi: 10.1038/s41467-018-07563-6. PMID:30498244 doi:http://dx.doi.org/10.1038/s41467-018-07563-6

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6gpe"

Categories: Escherichia coli K-12 | Large Structures | Hartig JS | Mayans O | Williams RM

@@ Line 1: / Line 1: @@
 ==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 ==
-<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='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'>[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='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>
 == 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 ==
@@ Line 22: / Line 22: @@
 __TOC__
 </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]]

6gpe

From Proteopedia

Revision as of 06:53, 8 February 2023

Crystal Structure of the CsiD Glutarate Hydroxylase

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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