Porphobilinogen deaminase and its structural similarity to the bidomain binding proteins

1993 ◽  
Vol 3 (3) ◽  
pp. 401-408 ◽  
Author(s):  
Gordon V. Louie
2007 ◽  
Vol 65 (4) ◽  
pp. 995-1005 ◽  
Author(s):  
Ganesh Natrajan ◽  
David R. Hall ◽  
Alex C. Thompson ◽  
Irina Gutsche ◽  
Laurent Terradot

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 288
Author(s):  
Victor Muleya ◽  
Claudius Marondedze

RNA-binding proteins (RBPs) are typical proteins that bind RNA through single or multiple RNA-binding domains (RBDs). These proteins have a functional role in determining the fate or function of the bound RNAs. A few hundred RBPs were known through in silico prediction based on computational assignment informed by structural similarity and the presence of classical RBDs. However, RBPs lacking such conventional RBDs were omitted. Owing to the recent mRNA interactome capture technology based on UV-crosslinking and fixing proteins to their mRNA targets followed by affinity capture purification and identification of RBPs by tandem mass spectrometry, several hundreds of RBPs have recently been discovered. These proteome-wide studies have colossally increased the number of proteins implicated in RNA binding and unearthed hundreds of novel RBPs lacking classical RBDs, such as proteins involved in intermediary metabolism. These discoveries provide wide insights into the post-transcriptional gene regulation players and their role in plant signaling, such as environmental stress conditions. In this review, novel discoveries of RBPs are explored, particularly on the evolving knowledge of their role in stress responses. The molecular functions of these RBPs, particularly focusing on those that do not have classical RBDs, are also elucidated at the systems level.


1989 ◽  
Vol 22 (1) ◽  
pp. 67-70 ◽  
Author(s):  
A. Bignami ◽  
W.S. Lane ◽  
D. Andrews ◽  
D. Dahl

2012 ◽  
Vol 194 (18) ◽  
pp. 5091-5100 ◽  
Author(s):  
Michele Girfoglio ◽  
Mosé Rossi ◽  
Raffaele Cannio

ABSTRACTA sequence encoding a putative extracellular endoglucanase (sso1354) was identified in the complete genome sequence ofSulfolobus solfataricus. The encoded protein shares signature motifs with members of glycoside hydrolases family 12. After an unsuccessful first attempt at cloning the full-length coding sequences inEscherichia coli, an active but unstable recombinant enzyme lacking a 27-residue N-terminal sequence was generated. This 27-amino-acid sequence shows significant similarity with corresponding regions in the sugar binding proteins AraS, GlcS, and TreS ofS. solfataricusthat are responsible for anchoring them to the plasma membrane. A strategy based on an effective vector/host genetic system forSulfolobusand on expression control by the promoter of theS. solfataricusgene which encodes the glucose binding protein allowed production of the enzyme in sufficient quantities for study. In fact, the enzyme expressed inS. solfataricuswas stable and highly thermoresistant and showed optimal activity at low pH and high temperature. The protein was detected mainly in the plasma membrane fraction, confirming the structural similarity to the sugar binding proteins. The results of the protein expression in the two different hosts showed that the SSO1354 enzyme is endowed with an endo-β-1-4-glucanase activity and specifically hydrolyzes cellulose. Moreover, it also shows significant but distinguishable specificity toward several other sugar polymers, such as lichenan, xylan, debranched arabinan, pachyman, and curdlan.


2022 ◽  
Vol 23 (2) ◽  
pp. 768
Author(s):  
Martin Bartas ◽  
Kristyna Slychko ◽  
Václav Brázda ◽  
Jiří Červeň ◽  
Christopher A. Beaudoin ◽  
...  

Z-DNA and Z-RNA are functionally important left-handed structures of nucleic acids, which play a significant role in several molecular and biological processes including DNA replication, gene expression regulation and viral nucleic acid sensing. Most proteins that have been proven to interact with Z-DNA/Z-RNA contain the so-called Zα domain, which is structurally well conserved. To date, only eight proteins with Zα domain have been described within a few organisms (including human, mouse, Danio rerio, Trypanosoma brucei and some viruses). Therefore, this paper aimed to search for new Z-DNA/Z-RNA binding proteins in the complete PDB structures database and from the AlphaFold2 protein models. A structure-based similarity search found 14 proteins with highly similar Zα domain structure in experimentally-defined proteins and 185 proteins with a putative Zα domain using the AlphaFold2 models. Structure-based alignment and molecular docking confirmed high functional conservation of amino acids involved in Z-DNA/Z-RNA, suggesting that Z-DNA/Z-RNA recognition may play an important role in a variety of cellular processes.


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