scholarly journals Dissecting the structural and functional roles of a vicinal iron-binding site in encapsulated ferritins

2019 ◽  
Author(s):  
Cecilia Piergentili ◽  
Jennifer Ross ◽  
Didi He ◽  
Kelly J. Gallagher ◽  
Will A. Stanley ◽  
...  
Keyword(s):  
Binding Site ◽  
Metal Binding ◽  
Rhodospirillum Rubrum ◽  
Catalytic Mechanism ◽  
Iron Oxidation ◽  
Functional Study ◽  
Secondary Site ◽  
Iron Store ◽  
Entry Site ◽  
Ferroxidase Center

AbstractEncapsulated ferritins belong to the universally distributed ferritin superfamily, which function as iron detoxification and storage systems. Encapsulated ferritins have a distinct annular structure and must associate with an encapsulin nanocage to form a competent iron store that is capable of holding significantly more iron than classical ferritins. The catalytic mechanism of iron oxidation in the ferritin family is still an open question, due to differences in organization of the ferroxidase catalytic site and secondary metal binding sites vicinal to this. We have previously identified a metal binding site on the inner surface of the Rhodospirillum rubrum encapsulated ferritin at the interface between the two-helix subunits and proximal to the ferroxidase center. Here we present a comprehensive structural and functional study to investigate the functional relevance of this proposed iron entry site by means of enzymatic assays, mass-spectrometry, and X-ray crystallography. We show that catalysis occurs in the ferroxidase center and suggest a dual role for the secondary site, which both serves to attract metal ions to the ferroxidase center and acts as a flow-restricting valve to limit the activity of the ferroxidase center. Moreover, confinement of encapsulated ferritins within the encapsulin nanocage, while enhancing the ability of the encapsulated ferritin to undergo catalysis, does not influence the function of the secondary site.

scholarly journals Dissecting the structural and functional roles of a putative metal entry site in encapsulated ferritins

2020 ◽  
Vol 295 (46) ◽  
pp. 15511-15526
Author(s):  
Cecilia Piergentili ◽  
Jennifer Ross ◽  
Didi He ◽  
Kelly J. Gallagher ◽  
Will A. Stanley ◽  
...  
Keyword(s):  
Metal Binding ◽  
Rhodospirillum Rubrum ◽  
Catalytic Mechanism ◽  
Iron Oxidation ◽  
Functional Study ◽  
Secondary Site ◽  
Iron Store ◽  
Entry Site ◽  
X Ray Crystallography ◽  
Ferroxidase Center

Encapsulated ferritins belong to the universally distributed ferritin superfamily, whose members function as iron detoxification and storage systems. Encapsulated ferritins have a distinct annular structure and must associate with an encapsulin nanocage to form a competent iron store that is capable of holding significantly more iron than classical ferritins. The catalytic mechanism of iron oxidation in the ferritin family is still an open question because of the differences in organization of the ferroxidase catalytic site and neighboring secondary metal-binding sites. We have previously identified a putative metal-binding site on the inner surface of the Rhodospirillum rubrum encapsulated ferritin at the interface between the two-helix subunits and proximal to the ferroxidase center. Here we present a comprehensive structural and functional study to investigate the functional relevance of this putative iron-entry site by means of enzymatic assays, MS, and X-ray crystallography. We show that catalysis occurs in the ferroxidase center and suggest a dual role for the secondary site, which both serves to attract metal ions to the ferroxidase center and acts as a flow-restricting valve to limit the activity of the ferroxidase center. Moreover, confinement of encapsulated ferritins within the encapsulin nanocage, although enhancing the ability of the encapsulated ferritin to undergo catalysis, does not influence the function of the secondary site. Our study demonstrates a novel molecular mechanism by which substrate flux to the ferroxidase center is controlled, potentially to ensure that iron oxidation is productively coupled to mineralization.

scholarly journals Conservation of the structural and functional architecture of encapsulated ferritins in bacteria and archaea

2019 ◽  
Vol 476 (6) ◽  
pp. 975-989 ◽  
Author(s):  
Didi He ◽  
Cecilia Piergentili ◽  
Jennifer Ross ◽  
Emma Tarrant ◽  
Laura R. Tuck ◽  
...  
Keyword(s):  
Metal Binding ◽  
Rhodospirillum Rubrum ◽  
Quaternary Structure ◽  
Pyrococcus Furiosus ◽  
Large Family ◽  
Native Mass Spectrometry ◽  
Wide Distribution ◽  
Iron Store ◽  
Unusual Structure ◽  
Ferroxidase Activity

Abstract Ferritins are a large family of intracellular proteins that protect the cell from oxidative stress by catalytically converting Fe(II) into less toxic Fe(III) and storing iron minerals within their core. Encapsulated ferritins (EncFtn) are a sub-family of ferritin-like proteins, which are widely distributed in all bacterial and archaeal phyla. The recently characterized Rhodospirillum rubrum EncFtn displays an unusual structure when compared with classical ferritins, with an open decameric structure that is enzymatically active, but unable to store iron. This EncFtn must be associated with an encapsulin nanocage in order to act as an iron store. Given the wide distribution of the EncFtn family in organisms with diverse environmental niches, a question arises as to whether this unusual structure is conserved across the family. Here, we characterize EncFtn proteins from the halophile Haliangium ochraceum and the thermophile Pyrococcus furiosus, which show the conserved annular pentamer of dimers topology. Key structural differences are apparent between the homologues, particularly in the centre of the ring and the secondary metal-binding site, which is not conserved across the homologues. Solution and native mass spectrometry analyses highlight that the stability of the protein quaternary structure differs between EncFtn proteins from different species. The ferroxidase activity of EncFtn proteins was confirmed, and we show that while the quaternary structure around the ferroxidase centre is distinct from classical ferritins, the ferroxidase activity is still inhibited by Zn(II). Our results highlight the common structural organization and activity of EncFtn proteins, despite diverse host environments and contexts within encapsulins.

Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication

2019 ◽  
Vol 476 (21) ◽  
pp. 3333-3353 ◽  
Author(s):  
Malti Yadav ◽  
Kamalendu Pal ◽  
Udayaditya Sen
Keyword(s):  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Triosephosphate Isomerase ◽  
Catalytic Mechanism ◽  
Degradation Mechanism ◽  
Structural Basis ◽  
Conserved Residues ◽  
Phosphodiester Bond ◽  
Cyclic Dinucleotides

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

scholarly journals Discovery of fungal surface NADases predominantly present in pathogenic species

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Øyvind Strømland ◽  
Juha P. Kallio ◽  
Annica Pschibul ◽  
Renate H. Skoge ◽  
Hulda M. Harðardóttir ◽  
...  
Keyword(s):  
Cell Death ◽  
Aspergillus Fumigatus ◽  
Neurospora Crassa ◽  
Binding Site ◽  
Host Cell ◽  
Nicotinamide Adenine Dinucleotide ◽  
Catalytic Mechanism ◽  
Pathogenic Species ◽  
X Ray ◽  
Cellular Bioenergetics

AbstractNicotinamide adenine dinucleotide (NAD) is a key molecule in cellular bioenergetics and signalling. Various bacterial pathogens release NADase enzymes into the host cell that deplete the host’s NAD+ pool, thereby causing rapid cell death. Here, we report the identification of NADases on the surface of fungi such as the pathogen Aspergillus fumigatus and the saprophyte Neurospora crassa. The enzymes harbour a tuberculosis necrotizing toxin (TNT) domain and are predominately present in pathogenic species. The 1.6 Å X-ray structure of the homodimeric A. fumigatus protein reveals unique properties including N-linked glycosylation and a Ca2+-binding site whose occupancy regulates activity. The structure in complex with a substrate analogue suggests a catalytic mechanism that is distinct from those of known NADases, ADP-ribosyl cyclases and transferases. We propose that fungal NADases may convey advantages during interaction with the host or competing microorganisms.

Unraveling the Substrate−Metal Binding Site of Ferrochelatase:  An X-ray Absorption Spectroscopic Study†

Biochemistry ◽  
2002 ◽  
Vol 41 (15) ◽  
pp. 4809-4818 ◽  
Author(s):  
Gloria C. Ferreira ◽  
Ricardo Franco ◽  
Arianna Mangravita ◽  
Graham N. George
Keyword(s):  
Spectroscopic Study ◽  
Binding Site ◽  
Metal Binding ◽  
Metal Binding Site ◽  
X Ray ◽  
Substrate Metal ◽  
X Ray Absorption

Construction of an additional metal-binding site in human metallothionein-2

2006 ◽  
Vol 101 (4) ◽  
pp. 354-360 ◽  
Author(s):  
Mitsutoshi Toyama ◽  
Mariko Sasaki ◽  
Noriaki Hirayama ◽  
Yoshikatsu Murooka ◽  
Mitsuo Yamashita
Keyword(s):  
Binding Site ◽  
Metal Binding ◽  
Metal Binding Site
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