Crystal Structure of Bacillus subtilis Cysteine Desulfurase SufS and Its Dynamic Interaction with Frataxin and Scaffold Protein SufU

Blauenburg, Bastian; Mielcarek, Andreas; Altegoer, Florian; Fage, Christopher D.; Linne, Uwe; Bange, Gert; Marahiel, Mohamed A.

doi:10.1371/journal.pone.0158749

Cited by 26 publications

(36 citation statements)

References 67 publications

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“…All the NifS structures were solved by molecular replacement using Molrep with a T. maritima NifS‐like protein (PDB ID: http://www.rcsb.org/pdb/search/structidSearch.do?structureId=1ECX) as a search model. The B. subtilis SufS structure was also solved by molecular replacement using previously determined B. subtilis SufS (PDB ID: http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5J8Q) . Models were built using COOT and refined using Refmac5 44 and PHENIX .…”

Section: Methodsmentioning

confidence: 99%

“…Indeed, this loop was shown to be disordered in previous studies on the crystal structures of type I cysteine desulfurase enzymes . On the other hand, the corresponding loop of type II cysteine desulfurase SufS is formed as an α‐helix in the resting state, which has been visualized by X‐ray crystal structure analysis .…”

Section: Introductionmentioning

confidence: 93%

“…The loop of Hy. thermophila NifS formed a twisted b-sheet, in which the conserved nucleophilic cysteine was located away from the PLP site by 23 A (Figs 2A and 3A). This conformation of the loop cannot allow the nucleophilic cysteine residue to attack substrate L-cysteine.…”

Section: Structural Visualization Of the Catalytic Loop Of A Type I Cmentioning

confidence: 99%

“…Importantly, the catalytic cysteine residue remained separated from the PLP site by 23 A not only in the resting state ( Fig. 3A) and the persulfurated form ( Fig.…”

Section: Possible Structural Change Of the Catalytic Loop In Type I Cmentioning

confidence: 99%

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Snapshots of PLP‐substrate and PLP‐product external aldimines as intermediates in two types of cysteine desulfurase enzymes

et al. 2019

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Cysteine desulfurase enzymes catalyze sulfur mobilization from l‐cysteine to sulfur‐containing biomolecules such as iron‐sulfur (Fe‐S) clusters and thio‐tRNAs. The enzymes utilize the cofactor pyridoxal‐5'‐phosphate (PLP), which forms the external substrate‐ and product‐aldimines and ketimines during catalysis and are grouped into two types (I and II) based on their different catalytic loops. To clarify the structure‐based catalytic mechanisms for each group, we determined the structures of the external substrate‐ and product‐aldimines as catalytic intermediates of NifS (type I) and SufS (type II) that are involved in Fe‐S cluster biosynthesis using X‐ray crystallographic snapshot analysis. As a common intermediate structure, the thiol group of the PLP‐l‐cysteine external aldimine is stabilized by the conserved histidine adjacent to PLP through a polar interaction. This interaction makes the thiol group orientated for subsequent nucleophilic attack by a conserved cysteine residue on the catalytic loop in the state of PLP‐l‐cysteine ketimine, which is formed from the PLP‐l‐cysteine aldimine. Unlike the intermediates, structural changes of the loops were different between the type I and II enzymes. In the type I enzyme, conformational and topological change of the loop is necessary for nucleophilic attack by the cysteine. In contrast, the loop in type II cysteine desulfurase enzymes showed no large conformational change; rather, it might possibly orient the thiol group of the catalytic cysteine for nucleophilic attack toward PLP‐l‐cysteine. The present structures allow a revision of the catalytic mechanism and may provide a clue for consideration of enzyme function, structural diversity, and evolution of cysteine desulfurase enzymes. Database Structural data are available in PDB database under the accession numbers http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5WT2, http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5WT4, http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5ZSP, http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5ZST, http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5ZS9, http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5ZSK, http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5ZSO, http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6KFZ, http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6KG0, and http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6KG1.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 93%

Section: Structural Visualization Of the Catalytic Loop Of A Type I Cmentioning

confidence: 99%

“…Importantly, the catalytic cysteine residue remained separated from the PLP site by 23 A not only in the resting state ( Fig. 3A) and the persulfurated form ( Fig.…”

Section: Possible Structural Change Of the Catalytic Loop In Type I Cmentioning

confidence: 99%

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Snapshots of PLP‐substrate and PLP‐product external aldimines as intermediates in two types of cysteine desulfurase enzymes

et al. 2019

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“…In bacteria, three multiprotein systems which are nitrogen fixation (NIF), iron-sulfur cluster (ISC), and mobilization of sulfur (SUF) are involved in the [Fe-S] cluster assembly, in which various CDSs are essential to transfer sulfur from free cysteine to diverse sulfur intermediate acceptors such as TusA, IscU, SufE, SufU, and CsdE [5, 11–13]. …”

Section: Introductionmentioning

confidence: 99%

Catalytic Intermediate Crystal Structures of Cysteine Desulfurase from the Archaeon Thermococcus onnurineus NA1

Huynh

Nguyen

et al. 2017

Archaea

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Thermococcus onnurineus NA1 is an anaerobic archaeon usually found in a deep-sea hydrothermal vent area, which can use elemental sulfur (S0) as a terminal electron acceptor for energy. Sulfur, essential to many biomolecules such as sulfur-containing amino acids and cofactors including iron-sulfur cluster, is usually mobilized from cysteine by the pyridoxal 5′-phosphate- (PLP-) dependent enzyme of cysteine desulfurase (CDS). We determined the crystal structures of CDS from Thermococcus onnurineus NA1 (ToCDS), which include native internal aldimine (NAT), gem-diamine (GD) with alanine, internal aldimine structure with existing alanine (IAA), and internal aldimine with persulfide-bound Cys356 (PSF) structures. The catalytic intermediate structures showed the dihedral angle rotation of Schiff-base linkage relative to the PLP pyridine ring. The ToCDS structures were compared with bacterial CDS structures, which will help us to understand the role and catalytic mechanism of ToCDS in the archaeon Thermococcus onnurineus NA1.

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FeSCluster Assembly:SUFSystem in Bacteria, Plastids and Archaea

Dong

Witcher

Outten

et al. 2017

Encyclopedia of Inorganic and Bioinorganic Chemistry

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Iron–sulfur (Fe–S) clusters are essential cofactors in biology due to their use in critical pathways such as nitrogen fixation, photosynthesis, and respiration. Fe–S cluster biogenesis requires complex systems to mobilize iron and sulfide, assemble the nascent cluster, and target Fe–S clusters to downstream target proteins. All of these steps must be coordinated to protect Fe–S cluster biogenesis intermediates from reactive oxygen species and other stressors. Multiple Fe–S cluster biogenesis pathways exist in different organisms and organelles. The Suf ( su lfur f ormation) pathway is phylogenetically the most ancient of the cluster biogenesis systems and is distributed across all domains of life. It can be found as the primary Fe–S cluster biogenesis pathway or as an auxiliary pathway adapted to maintain Fe–S cluster metabolism under stress conditions. Here we describe the biochemical, genetic, and physiological characterization of the Suf system, in all of its iterations.

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Crystal Structure of Bacillus subtilis Cysteine Desulfurase SufS and Its Dynamic Interaction with Frataxin and Scaffold Protein SufU

Cited by 26 publications

References 67 publications

Snapshots of PLP‐substrate and PLP‐product external aldimines as intermediates in two types of cysteine desulfurase enzymes

Snapshots of PLP‐substrate and PLP‐product external aldimines as intermediates in two types of cysteine desulfurase enzymes

Catalytic Intermediate Crystal Structures of Cysteine Desulfurase from the Archaeon Thermococcus onnurineus NA1

FeSCluster Assembly:SUFSystem in Bacteria, Plastids and Archaea

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