scholarly journals Crystal Structure of tRNA Adenosine Deaminase (TadA) fromAquifex aeolicus

2005 ◽  
Vol 280 (16) ◽  
pp. 16002-16008 ◽  
Author(s):  
Mitsuo Kuratani ◽  
Ryohei Ishii ◽  
Yoshitaka Bessho ◽  
Ryuya Fukunaga ◽  
Toru Sengoku ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Adenosine Deaminase ◽  
Cytosine Deaminase ◽  
Amino Acid Residues ◽  
Aquifex Aeolicus ◽  
Stem Loop ◽  
Dimeric Structure ◽  
Docking Model ◽  
Tetrameric Structure ◽  
Yeast Cytosine Deaminase

The bacterial tRNA adenosine deaminase (TadA) generates inosine by deaminating the adenosine residue at the wobble position of tRNAArg-2. This modification is essential for the decoding system. In this study, we determined the crystal structure ofAquifex aeolicusTadA at a 1.8-Å resolution. This is the first structure of a deaminase acting on tRNA.A. aeolicusTadA has an α/β/α three-layered fold and forms a homodimer. TheA. aeolicusTadA dimeric structure is completely different from the tetrameric structure of yeast CDD1, which deaminates mRNA and cytidine, but is similar to the dimeric structure of yeast cytosine deaminase. However, in theA. aeolicusTadA structure, the shapes of the C-terminal helix and the regions between the β4 and β5 strands are quite distinct from those of yeast cytosine deaminase and a large cavity is produced. This cavity contains many conserved amino acid residues that are likely to be involved in either catalysis or tRNA binding. We made a docking model of TadA with the tRNA anticodon stem loop.

scholarly journals Crystal Structure of Yeast Cytosine Deaminase

2003 ◽  
Vol 278 (21) ◽  
pp. 19111-19117 ◽  
Author(s):  
Tzu-Ping Ko ◽  
Jing-Jer Lin ◽  
Chih-Yung Hu ◽  
Yi-Hsin Hsu ◽  
Andrew H.-J. Wang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Cytosine Deaminase ◽  
Yeast Cytosine Deaminase

scholarly journals The 1.14 Å Crystal Structure of Yeast Cytosine Deaminase

Structure ◽  
2003 ◽  
Vol 11 (8) ◽  
pp. 961-972 ◽  
Author(s):  
Gregory C Ireton ◽  
Margaret E Black ◽  
Barry L Stoddard
Keyword(s):  
Crystal Structure ◽  
Cytosine Deaminase ◽  
Yeast Cytosine Deaminase

scholarly journals Crystal structure of yeast monothiol glutaredoxin Grx6 in complex with a glutathione-coordinated [2Fe–2S] cluster

2016 ◽  
Vol 72 (10) ◽  
pp. 732-737 ◽  
Author(s):  
Mohnad Abdalla ◽  
Ya-Nan Dai ◽  
Chang-Biao Chi ◽  
Wang Cheng ◽  
Dong-Dong Cao ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Saccharomyces Cerevisiae ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Active Site ◽  
Binding Pattern ◽  
Biological Functions ◽  
Structural Comparison ◽  
Multiple Sequence ◽  
Dimeric Structure

Glutaredoxins (Grxs) constitute a superfamily of proteins that perform diverse biological functions. TheSaccharomyces cerevisiaeglutaredoxin Grx6 not only serves as a glutathione (GSH)-dependent oxidoreductase and as a GSH transferase, but also as an essential [2Fe–2S]-binding protein. Here, the dimeric structure of the C-terminal domain of Grx6 (holo Grx6C), bridged by one [2Fe–2S] cluster coordinated by the active-site Cys136 and two external GSH molecules, is reported. Structural comparison combined with multiple-sequence alignment demonstrated that holo Grx6C is similar to the [2Fe–2S] cluster-incorporated dithiol Grxs, which share a highly conserved [2Fe–2S] cluster-binding pattern and dimeric conformation that is distinct from the previously identified [2Fe–2S] cluster-ligated monothiol Grxs.

scholarly journals Mapping the Contact Sites of the Escherichia coli Division-Initiating Proteins FtsZ and ZapA by BAMG Cross-Linking and Site-Directed Mutagenesis

2018 ◽  
Vol 19 (10) ◽  
pp. 2928 ◽  
Author(s):  
Winfried Roseboom ◽  
Madhvi Nazir ◽  
Nils Meiresonne ◽  
Tamimount Mohammadi ◽  
Jolanda Verheul ◽  
...  
Keyword(s):  
Site Directed Mutagenesis ◽  
Cross Linking ◽  
Directed Mutagenesis ◽  
Amino Acid Residues ◽  
Binding Interface ◽  
Tetrameric Structure ◽  
Z Ring ◽  
Cross Links ◽  
Chemical Cross Linking

Cell division in bacteria is initiated by the polymerization of FtsZ at midcell in a ring-like structure called the Z-ring. ZapA and other proteins assist Z-ring formation and ZapA binds ZapB, which senses the presence of the nucleoids. The FtsZ–ZapA binding interface was analyzed by chemical cross-linking mass spectrometry (CXMS) under in vitro FtsZ-polymerizing conditions in the presence of GTP. Amino acids residue K42 from ZapA was cross-linked to amino acid residues K51 and K66 from FtsZ, close to the interphase between FtsZ molecules in protofilaments. Five different cross-links confirmed the tetrameric structure of ZapA. A number of FtsZ cross-links suggests that its C-terminal domain of 55 residues, thought to be largely disordered, has a limited freedom to move in space. Site-directed mutagenesis of ZapA reveals an interaction site in the globular head of the protein close to K42. Using the information on the cross-links and the mutants that lost the ability to interact with FtsZ, a model of the FtsZ protofilament–ZapA tetramer complex was obtained by information-driven docking with the HADDOCK2.2 webserver.

Crystal structure of Aquifex aeolicus gene product Aq1627: a putative phosphoglucosamine mutase reveals a unique C-terminal end-to-end disulfide linkage

2017 ◽  
Vol 13 (7) ◽  
pp. 1370-1376
Author(s):  
Upasana Sridharan ◽  
Seiki Kuramitsu ◽  
Shigeyuki Yokoyama ◽  
Thirumananseri Kumarevel ◽  
Karthe Ponnuraj
Keyword(s):  
Crystal Structure ◽  
Gene Product ◽  
Aquifex Aeolicus ◽  
Disulfide Linkage ◽  
Hyperthermophilic Bacterium ◽  
End To End

The crystal structure of Aq1627 protein from Aquifex aeolicus, a hyperthermophilic bacterium has been solved, which reveals a unique end-to-end disulfide linkage.

Protein-Programmed Accumulation of Yeast Cytosine Deaminase in Cancer Cells in Response to Mock-Hypoxia

2019 ◽  
Vol 8 (5) ◽  
pp. 948-954 ◽  
Author(s):  
Tiana D. Warren ◽  
Krishna Patel ◽  
James R. Eshleman ◽  
Marc Ostermeier
Keyword(s):  
Cancer Cells ◽  
Cytosine Deaminase ◽  
Yeast Cytosine Deaminase

scholarly journals Characterization and Incidence of the First Member of the Genus Mitovirus Identified in the Phytopathogenic Species Fusarium oxysporum

Viruses ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 279 ◽  
Author(s):  
Almudena Torres-Trenas ◽  
Encarnación Pérez-Artés
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Genetic Code ◽  
Fusarium Oxysporum ◽  
Amino Acid Residues ◽  
Fusarium Spp ◽  
Stem Loop ◽  
Universal Genetic Code ◽  
The Family ◽  
Amino Acid Tryptophan

A novel mycovirus named Fusarium oxysporum f. sp. dianthi mitovirus 1 (FodMV1) has been identified infecting a strain of Fusarium oxysporum f. sp. dianthi from Colombia. The genome of FodMV1 is 2313 nt long, and comprises a 172-nt 5’-UTR, a 2025-nt single ORF encoding an RdRp of 675 amino acid residues, and a 113-nt 3´-UTR. Homology BlastX searches identifies FodMV1 as a novel member of the genus Mitovirus in the family Narnaviridae. As the rest of mitoviruses, the genome of FodMV1 presents a high percentage of A+U (58.8%) and contains a number of UGA codons that encode the amino acid tryptophan rather than acting as stop codons as in the universal genetic code. Another common feature with other mitoviruses is that the 5′- and 3′-UTR regions of FodMV1 can be folded into potentially stable stem-loop structures. Result from phylogenetic analysis place FodMV1 in a different clade than the rest of mitoviruses described in other Fusarium spp. Incidence of FodMV1-infections in the collection of F. oxysporum f. sp. dianthi isolates analyzed is relatively high. Of particular interest is the fact that FodMV1 has been detected infecting isolates from two geographical areas as distant as Spain and Colombia.

Crystal structure of ribosomal protein L1 from the bacterium Aquifex aeolicus

2011 ◽  
Vol 56 (4) ◽  
pp. 603-607 ◽  
Author(s):  
E. Yu. Nikonova ◽  
S. V. Tishchenko ◽  
A. G. Gabdulkhakov ◽  
A. A. Shklyaeva ◽  
M. B. Garber ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ribosomal Protein ◽  
Aquifex Aeolicus ◽  
Ribosomal Protein L1

scholarly journals Structure–function studies of human deoxyhypusine synthase: identification of amino acid residues critical for the binding of spermidine and NAD

2001 ◽  
Vol 355 (3) ◽  
pp. 841-849 ◽  
Author(s):  
Chang Hoon LEE ◽  
Patrick Y. UM ◽  
Myung Hee PARK
Keyword(s):  
Crystal Structure ◽  
Enzyme Activity ◽  
Amino Acid ◽  
Binding Sites ◽  
Binding Pocket ◽  
Complete Loss ◽  
Amino Acid Residues ◽  
Deoxyhypusine Synthase ◽  
Positive Identification ◽  
Insight Into

Deoxyhypusine synthase catalyses the first step in the biosynthesis of hypusine [Nε-(4-amino-2-hydroxybutyl)lysine]. The crystal structure of human deoxyhypusine synthase in complex with NAD revealed four NAD-binding sites per enzyme tetramer, and led to a prediction of the spermidine-binding pocket. We have replaced each of the seven amino acid residues at the predicted spermidine-binding site, and eleven residues that contact NAD, on an individual basis with alanine. Of the amino acid residues at the spermidine site, substitution of Asp-243, Trp-327, His-288, Asp-316 or Glu-323 with alanine caused an almost complete loss of spermidine binding and enzyme activity; only the mutation Tyr-305 → Ala showed partial binding and activity. His-288 → Ala was also deficient in terms of binding NAD. NAD binding was significantly reduced in all of the NAD-site mutant enzymes, except for Glu-137 → Ala, which showed a normal binding of NAD, but was totally lacking in spermidine binding. Of the NAD-site mutant enzymes, Asp-342 → Ala, Asp-313 → Ala and Asp-238 → Ala displayed the lowest binding of NAD. These enzymes and His-288Ala also showed a reduced binding of spermidine, presumably because spermidine binding is dependent on NAD. These findings permit the positive identification of amino acid residues critical for binding of spermidine and NAD, and provide a new insight into the complex molecular interactions involved in the deoxyhypusine synthase reaction.

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