7xel

From Proteopedia

(Difference between revisions)

Current revision

SufS soaked with D-penicillamine

Structural highlights

7xel is a 1 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SUFS_BACSU Enzyme able to deliver sulfur to partners involved in Fe-S cluster assembly. Catalyzes the removal of elemental sulfur atoms from L-cysteine to produce L-alanine. Activity is stimulated 40-to 100-fold by SufU, which acts as a second substrate for this enzyme following release of Ala, and generating SufU.S. A mixture of SufS, SufU, Fra and L-cysteine is able to reconstitute Fe-S clusters on apo-aconitase (citB), reconstituting aconitase activity.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The reactivity of pyridoxal-5'-phosphate (PLP) with cysteine and its derivatives has been of increasing interest because the corresponding product, a thiazolidine PLP-cysteine adduct, can be formed via PLP-dependent enzymatic and non-enzymatic reactions. Here, we report biochemical and X-ray crystallographic snapshots of thiazolidine formation in reaction of D-cysteine with PLP in SufS, a PLP-dependent L-cysteine desulfurase. By comparing L- and D-penicillamine-bound SufS showing no thiazolidine formation in the crystals with D-cysteine SufS, we proposed a thiazolidine formation mechanism with important factors: the polar environments provided by the carbonyl groups of Ala28-Ala29 and Lys224-mediated base catalysis for the nucleophilic thiolate of D-cysteine.

Visualizing thiazolidine ring formation in the reaction of D-cysteine and pyridoxal-5'-phosphate within L-cysteine desulfurase SufS.,Nakamura R, Fujishiro T Biochem Biophys Res Commun. 2025 Mar 25;754:151497. doi: , 10.1016/j.bbrc.2025.151497. Epub 2025 Feb 19. PMID:40020322^[4]

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

References

↑ Albrecht AG, Netz DJ, Miethke M, Pierik AJ, Burghaus O, Peuckert F, Lill R, Marahiel MA. SufU is an essential iron-sulfur cluster scaffold protein in Bacillus subtilis. J Bacteriol. 2010 Mar;192(6):1643-51. doi: 10.1128/JB.01536-09. Epub 2010 Jan 22. PMID:20097860 doi:http://dx.doi.org/10.1128/JB.01536-09
↑ Selbach B, Earles E, Dos Santos PC. Kinetic analysis of the bisubstrate cysteine desulfurase SufS from Bacillus subtilis. Biochemistry. 2010 Oct 12;49(40):8794-802. doi: 10.1021/bi101358k. Epub 2010 Sep , 16. PMID:20822158 doi:http://dx.doi.org/10.1021/bi101358k
↑ Albrecht AG, Landmann H, Nette D, Burghaus O, Peuckert F, Seubert A, Miethke M, Marahiel MA. The frataxin homologue Fra plays a key role in intracellular iron channeling in Bacillus subtilis. Chembiochem. 2011 Sep 5;12(13):2052-61. doi: 10.1002/cbic.201100190. Epub 2011, Jul 8. PMID:21744456 doi:http://dx.doi.org/10.1002/cbic.201100190
↑ Nakamura R, Fujishiro T. Visualizing thiazolidine ring formation in the reaction of D-cysteine and pyridoxal-5'-phosphate within L-cysteine desulfurase SufS. Biochem Biophys Res Commun. 2025 Mar 25;754:151497. PMID:40020322 doi:10.1016/j.bbrc.2025.151497

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/7xel"

Categories: Bacillus subtilis subsp. subtilis str. 168 | Large Structures | Fujishiro T | Nakamura R

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 7xel is ON HOLD
+==SufS soaked with D-penicillamine==
+<StructureSection load='7xel' size='340' side='right'caption='[[7xel]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7xel]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XEL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XEL 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]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=7xel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xel OCA], [https://pdbe.org/7xel PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xel RCSB], [https://www.ebi.ac.uk/pdbsum/7xel PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xel ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SUFS_BACSU SUFS_BACSU] Enzyme able to deliver sulfur to partners involved in Fe-S cluster assembly. Catalyzes the removal of elemental sulfur atoms from L-cysteine to produce L-alanine. Activity is stimulated 40-to 100-fold by SufU, which acts as a second substrate for this enzyme following release of Ala, and generating SufU.S. A mixture of SufS, SufU, Fra and L-cysteine is able to reconstitute Fe-S clusters on apo-aconitase (citB), reconstituting aconitase activity.<ref>PMID:20097860</ref> <ref>PMID:20822158</ref> <ref>PMID:21744456</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The reactivity of pyridoxal-5'-phosphate (PLP) with cysteine and its derivatives has been of increasing interest because the corresponding product, a thiazolidine PLP-cysteine adduct, can be formed via PLP-dependent enzymatic and non-enzymatic reactions. Here, we report biochemical and X-ray crystallographic snapshots of thiazolidine formation in reaction of D-cysteine with PLP in SufS, a PLP-dependent L-cysteine desulfurase. By comparing L- and D-penicillamine-bound SufS showing no thiazolidine formation in the crystals with D-cysteine SufS, we proposed a thiazolidine formation mechanism with important factors: the polar environments provided by the carbonyl groups of Ala28-Ala29 and Lys224-mediated base catalysis for the nucleophilic thiolate of D-cysteine.
-Authors:
+Visualizing thiazolidine ring formation in the reaction of D-cysteine and pyridoxal-5'-phosphate within L-cysteine desulfurase SufS.,Nakamura R, Fujishiro T Biochem Biophys Res Commun. 2025 Mar 25;754:151497. doi: , 10.1016/j.bbrc.2025.151497. Epub 2025 Feb 19. PMID:40020322<ref>PMID:40020322</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 7xel" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
+[[Category: Large Structures]]
+[[Category: Fujishiro T]]
+[[Category: Nakamura R]]

7xel

From Proteopedia

Current revision

SufS soaked with D-penicillamine

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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