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7uka

From Proteopedia

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YgiC from Escherichia coli K-12 in complex with ADP

Structural highlights

7uka is a 1 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.
Method:	X-ray diffraction, Resolution 2.2Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

YGIC_ECOLI May be a ligase forming an amide bond. Shows ATPase activity. Despite its similarity to the C-terminal synthetase domain of Gss, is not a glutathionylspermidine (Gsp) synthetase. Cannot synthesize Gsp, glutathione (GSH), or GSH intermediates, from GSH and spermidine, cysteine and glutamate, gamma-glutamylcysteine and spermidine, and gamma-glutamylcysteine and glycine. Does not bind to Gsp.^[1]

Publication Abstract from PubMed

Polyamines and polyamine-containing metabolites are involved in many cellular processes related to bacterial cell growth and survival. In Escherichia coli, the bifunctional enzyme glutathionylspermidine synthetase/amidase (GspSA) controls the production of glutathionylspermidine, which has a protective role against oxidative stress. E. coli also encodes two enzymes with homology to the synthetase domain of GspSA, YgiC, and YjfC; however, these do not catalyze the formation of glutathionylspermidine, and their catalytic function remained unknown. Here, we detail the structural and functional characterization of YgiC and YjfC. Using X-ray crystallography, the high-resolution crystal structures of YgiC and YjfC were obtained. This revealed that YgiC and YjfC possess multiple substitutions in key residues required for binding of glutathione in GspSA. Despite this difference, these enzymes share a similar active site structure to GspSA, suggesting that they catalyze the formation of an alternate peptide horizontal line spermidine conjugate. As the physiological substrates of YgiC and YjfC are unknown, this was probed using the peptide triglycine as a model substrate. A combination of enzyme activity assays and mass spectrometry revealed that YgiC and YjfC can function as peptide-spermidine ligases, forming a triglycine-spermidine conjugate. For both enzymes, conjugate formation was only observed in the presence of spermidine, but not other common polyamines, supporting that spermidine or a spermidine derivative is the physiological substrate. Importantly, since YgiC and YjfC are widely distributed in Gram-negative bacterial species, this suggests that these enzymes function in a conserved cellular process, representing a currently unknown aspect of bacterial polyamine metabolism.

Escherichia coli YgiC and YjfC Possess Peptide horizontal line Spermidine Ligase Activity.,Pederick JL, Klose J, Jovcevski B, Pukala TL, Bruning JB Biochemistry. 2023 Feb 6. doi: 10.1021/acs.biochem.2c00592. PMID:36745518^[2]

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

References

↑ Sui L, Warren JC, Russell JP, Stourman NV. Comparison of the functions of glutathionylspermidine synthetase/amidase from E. coli and its predicted homologues YgiC and YjfC. Int J Biochem Mol Biol. 2012;3(3):302-12. Epub 2012 Sep 25 PMID:23097746
↑ Pederick JL, Klose J, Jovcevski B, Pukala TL, Bruning JB. Escherichia coli YgiC and YjfC Possess Peptide─Spermidine Ligase Activity. Biochemistry. 2023 Feb 21;62(4):899-911. PMID:36745518 doi:10.1021/acs.biochem.2c00592

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/7uka"

Categories: Escherichia coli K-12 | Large Structures | Bruning JB | Pederick JL

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[7uka]] is a 1 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=7UKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UKA FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=7uka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uka OCA], [https://pdbe.org/7uka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uka RCSB], [https://www.ebi.ac.uk/pdbsum/7uka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uka ProSAT]</span></td></tr>
 </table>

7uka

From Proteopedia

Current revision

YgiC from Escherichia coli K-12 in complex with ADP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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