Structural diversity in metal ion chelation and the structure of uroporphyrinogen III synthase

2002 ◽  
Vol 30 (4) ◽  
pp. 595-600 ◽  
Author(s):  
H. L. Schubert ◽  
E. Raux ◽  
M. A. A. Matthews ◽  
J. D. Phillips ◽  
K. S. Wilson ◽  
...  
Keyword(s):  
Active Site ◽  
Metal Ion ◽  
Structural Diversity ◽  
Structural Similarity ◽  
Ring Closure ◽  
Catalytic Reactions ◽  
Central Metal ◽  
Tertiary Structures ◽  
Bacillus Subtilus ◽  
Metal Ion Chelation

All tetrapyrroles are synthesized through a branched pathway, and although each tetrapyrrole receives unique modifications around the ring periphery, they all share the unifying feature of a central metal ion. Each pathway maintains a unique metal ion chelatase, and several tertiary structures have been determined, including those of the protoporphyrin ferrochelatase from both human and Bacillus subtilus, and the cobalt chelatase CbiK. These enzymes exhibit strong structural similarity and appear to function by a similar mechanism. Met8p, from Saccharomyces cerevisiae, catalyses ferrochelation during the synthesis of sirohaem, and the structure reveals a novel chelatase architecture whereby both ferrochelation and NAD+-dependent dehydrogenation take place in a single bifunctional active site. Asp-141 appears to participate in both catalytic reactions. The final common biosynthetic step in tetrapyrrole biosynthesis is the generation of uroporphyrinogen by uroporphyrinogen III synthase, whereby the D ring of hydroxymethylbilane is flipped during ring closure to generate the asymmetrical structure of uroporphyrinogen III. The recently derived structure of uroporphyrinogen III synthase reveals a bi-lobed structure in which the active site lies between the domains.

Structural diversity in metal ion chelation, and the structure of uro'gen III synthase

2002 ◽  
Vol 30 (3) ◽  
pp. A48-A48
Author(s):  
H. L. Schubert ◽  
E. Raux ◽  
M. A. A. Mathews ◽  
J. D. Phillips ◽  
K. S. Wilson ◽  
...  
Keyword(s):  
Metal Ion ◽  
Structural Diversity ◽  
Metal Ion Chelation

scholarly journals Structural and biochemical characteristics of two Staphylococcus epidermidis RNase J paralogs RNase J1 and RNase J2

2020 ◽  
Vol 295 (49) ◽  
pp. 16863-16876
Author(s):  
Rishi Raj ◽  
Savitha Nadig ◽  
Twinkal Patel ◽  
Balasubramanian Gopal
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Staphylococcus Epidermidis ◽  
Metal Ion ◽  
Quaternary Structure ◽  
Structural Similarity ◽  
Endonuclease Activity ◽  
Metal Cofactor ◽  
Rna Maturation ◽  
Metal Cofactors

RNase J enzymes are metallohydrolases that are involved in RNA maturation and RNA recycling, govern gene expression in bacteria, and catalyze both exonuclease and endonuclease activity. The catalytic activity of RNase J is regulated by multiple mechanisms which include oligomerization, conformational changes to aid substrate recognition, and the metal cofactor at the active site. However, little is known of how RNase J paralogs differ in expression and activity. Here we describe structural and biochemical features of two Staphylococcus epidermidis RNase J paralogs, RNase J1 and RNase J2. RNase J1 is a homodimer with exonuclease activity aided by two metal cofactors at the active site. RNase J2, on the other hand, has endonuclease activity and one metal ion at the active site and is predominantly a monomer. We note that the expression levels of these enzymes vary across Staphylococcal strains. Together, these observations suggest that multiple interacting RNase J paralogs could provide a strategy for functional improvisation utilizing differences in intracellular concentration, quaternary structure, and distinct active site architecture despite overall structural similarity.

scholarly journals Active-Site Models of Streptococcus pyogenes Cas9 in DNA Cleavage State

2021 ◽  
Vol 8 ◽  
Author(s):  
Honghai Tang ◽  
Hui Yuan ◽  
Wenhao Du ◽  
Gan Li ◽  
Dongmei Xue ◽  
...  
Keyword(s):  
Active Site ◽  
Dna Cleavage ◽  
Metal Ion ◽  
Active Sites ◽  
Structural Similarity ◽  
Atomic Model ◽  
Nucleophilic Attack ◽  
Target Dna ◽  
Coordinated Water ◽  
Dna Complex

CRISPR-Cas9 is a powerful tool for target genome editing in living cells. Significant advances have been made to understand how this system cleaves target DNA. HNH is a nuclease domain, which shares structural similarity with the HNH endonuclease characterzied by a beta-beta-alpha-metal fold. Therefore, based on one- and two-metal-ion mechanisms, homology modeling and molecular dynamics (MD) simulation are suitable tools for building an atomic model of Cas9 in the DNA cleavage state. Here, by modeling and MD, we presented an atomic model of SpCas9–sgRNA–DNA complex with the cleavage state. This model shows that the HNH and RuvC conformations resemble their DNA cleavage state where the active-sites in the complex coordinate with DNA, Mg2+ ions, and water. Among them, residues D10, E762, H983, and D986 locate at the first shell of the RuvC active-site and interact with the ions directly, residues H982 or/and H985 are general (Lewis) bases, and the coordinated water is located at the positions for nucleophilic attack of the scissile phosphate. Meanwhile, this catalytic model led us to engineer a new SpCas9 variant (SpCas9-H982A + H983D) with reduced off-target effects. Thus, our study provided new mechanistic insights into the CRISPR-Cas9 system in the DNA cleavage state and offered useful guidance for engineering new CRISPR-Cas9 editing systems with improved specificity.

scholarly journals StructAnalyzer - a tool for sequence vs. structure similarity analysis

2017 ◽  
Vol 63 (4) ◽  
Author(s):  
Jakub Wiedemann ◽  
Maciej Miłostan
Keyword(s):  
Sequence Similarity ◽  
General Rule ◽  
Structural Diversity ◽  
Structural Similarity ◽  
Focus Attention ◽  
Rna Structures ◽  
Structural Variants ◽  
Tertiary Structures ◽  
Structure Similarity ◽  
Primary Structures

In the world of RNAs and proteins similarities on the level of primary structures of two comparable molecules usually correspond to structural similarities on the tertiary level. In other words, measures of sequence and structure similarities are in general correlated – high value of sequence similarity impose high value of structural similarity. However important exceptions  that stay in contrary with the general rule can be identified. It is possible to find similar structures with very different sequences and also similar sequences with very different structures. In this paper we focus attention on the latter case and propose  a tool, called StructAnalyzer, supporting analysis of relations between sequence and structure similarities. Recognition of diversity of tertiary structures of molecules with very similar primary structures may be the key for better understanding of mechanisms influencing folding of RNA or proteins and as result their function. StructAnalyzer allows exploration and visualization of structural diversity in relation to sequence similarity. We show how the tool can be used to screen RNA structures in PDB for sequences with structural variants.

scholarly journals Direct Measurement of Metal Ion Chelation in the Active Site of Human Ferrochelatase†

Biochemistry ◽  
2007 ◽  
Vol 46 (27) ◽  
pp. 8121-8127 ◽  
Author(s):  
M. Hoggins ◽  
H. A. Dailey ◽  
C. N. Hunter ◽  
J. D. Reid
Keyword(s):  
Direct Measurement ◽  
Active Site ◽  
Metal Ion ◽  
Metal Ion Chelation

Direct Measurement of Metal-Ion Chelation in the Active Site of the AAA+ATPase Magnesium Chelatase†

Biochemistry ◽  
2007 ◽  
Vol 46 (44) ◽  
pp. 12788-12794 ◽  
Author(s):  
Joanne Viney ◽  
Paul A. Davison ◽  
C. Neil Hunter ◽  
James D. Reid
Keyword(s):  
Direct Measurement ◽  
Active Site ◽  
Metal Ion ◽  
Magnesium Chelatase ◽  
Aaa Atpase ◽  
Metal Ion Chelation

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.

Protonation effects on dynamic flux properties of aqueous metal complexes

2009 ◽  
Vol 74 (10) ◽  
pp. 1543-1557 ◽  
Author(s):  
Herman P. Van Leeuwen ◽  
Raewyn M. Town
Keyword(s):  
Complex Formation ◽  
Metal Ion ◽  
Good Description ◽  
Minor Component ◽  
Outer Sphere ◽  
Metal Species ◽  
Central Metal ◽  
Inner Sphere ◽  
A Minor ◽  
Protonated Ligand

The degree of (de)protonation of aqueous metal species has significant consequences for the kinetics of complex formation/dissociation. All protonated forms of both the ligand and the hydrated central metal ion contribute to the rate of complex formation to an extent weighted by the pertaining outer-sphere stabilities. Likewise, the lifetime of the uncomplexed metal is determined by all the various protonated ligand species. Therefore, the interfacial reaction layer thickness, μ, and the ensuing kinetic flux, Jkin, are more involved than in the conventional case. All inner-sphere complexes contribute to the overall rate of dissociation, as weighted by their respective rate constants for dissociation, kd. The presence of inner-sphere deprotonated H2O, or of outer-sphere protonated ligand, generally has a great impact on kd of the inner-sphere complex. Consequently, the overall flux can be dominated by a species that is a minor component of the bulk speciation. The concepts are shown to provide a good description of experimental stripping chronopotentiometric data for several protonated metal–ligand systems.

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