scholarly journals Crystal Structures of Two Isozymes of Citrate Synthase fromSulfolobus tokodaiiStrain 7

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Midori Murakami ◽  
Tsutomu Kouyama
Keyword(s):  
Crystal Structures ◽  
Thermal Inactivation ◽  
Citrate Synthase ◽  
Ion Pairs ◽  
Thermal Adaptation ◽  
Structural Comparison ◽  
Thermophilic Microorganisms ◽  
Sulfolobus Tokodaii ◽  
Sequence Identity ◽  
Adaptation Mechanisms

Thermoacidophilic archaeonSulfolobus tokodaiistrain 7 has two citrate synthase genes (ST1805-CS and ST0587-CS) in the genome with 45% sequence identity. Because they exhibit similar optimal temperatures of catalytic activity and thermal inactivation profiles, we performed structural comparisons between these isozymes to elucidate adaptation mechanisms to high temperatures in thermophilic CSs. The crystal structures of ST1805-CS and ST0587-CS were determined at 2.0 Å and 2.7 Å resolutions, respectively. Structural comparison reveals that both of them are dimeric enzymes composed of two identical subunits, and these dimeric structures are quite similar to those of citrate synthases from archaea and eubacteria. ST0587-CS has, however, 55 ion pairs within whole dimer structure, while having only 36 in ST1805-CS. Although the number and distributions of ion pairs are distinct from each other, intersubunit ion pairs between two domains of each isozyme are identical especially in interterminal region. Because the location and number of ion pairs are in a trend with other CSs from thermophilic microorganisms, the factors responsible for thermal adaptation of ST-CS isozymes are characterized by ion pairs in interterminal region.

scholarly journals 2P014 Crystal structures of two isozymes of citrate synthase from Sulfolobus tokodaii

2004 ◽  
Vol 44 (supplement) ◽  
pp. S113
Author(s):  
M. Murakami ◽  
K. Ihara ◽  
T. Kouyama
Keyword(s):  
Crystal Structures ◽  
Citrate Synthase ◽  
Sulfolobus Tokodaii

scholarly journals Pyrethroid Carboxylesterase PytH from Sphingobium faniae JZ-2: Structure and Catalytic Mechanism

2020 ◽  
Vol 86 (12) ◽  
Author(s):  
Dongqing Xu ◽  
Yanyan Gao ◽  
Bo Sun ◽  
Tingting Ran ◽  
Liangping Zeng ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Catalytic Mechanism ◽  
Hydrophobic Pocket ◽  
Core Domain ◽  
Content Type ◽  
Sequence Identity ◽  
Hydrolase Fold ◽  
Wide Range ◽  
Pyrethroid Pesticides ◽  
Lid Domain

ABSTRACT Carboxylesterase PytH, isolated from the pyrethroid-degrading bacterium Sphingobium faniae JZ-2, could rapidly hydrolyze the ester bond of a wide range of pyrethroid pesticides, including permethrin, fenpropathrin, cypermethrin, fenvalerate, deltamethrin, cyhalothrin, and bifenthrin. To elucidate the catalytic mechanism of PytH, we report here the crystal structures of PytH with bifenthrin (BIF) and phenylmethylsulfonyl fluoride (PMSF) and two PytH mutants. Though PytH shares low sequence identity with reported α/β-hydrolase fold proteins, the typical triad catalytic center with Ser-His-Asp triad (Ser78, His230, and Asp202) is present and vital for the hydrolase activity. However, no contact was found between Ser78 and His230 in the structures we solved, which may be due to the fact that the PytH structures we determined are in their inactive or low-activity forms. The structure of PytH is composed of a core domain and a lid domain; some hydrophobic amino acid residues surrounding the substrate from both domains form a deeper and wider hydrophobic pocket than its homologous structures. This indicates that the larger hydrophobic pocket makes PytH fit for its larger substrate binding; both lid and core domains are involved in substrate binding, and the lid domain-induced core domain movement may make the active center correctly positioned with substrates. IMPORTANCE Pyrethroid pesticides are widely applied in agriculture and household; however, extensive use of these pesticides also causes serious environmental and health problems. The hydrolysis of pyrethroids by carboxylesterases is the major pathway of microbial degradation of pyrethroids, but the structure of carboxylesterases and its catalytic mechanism are still unknown. Carboxylesterase PytH from Sphingobium faniae JZ-2 could effectively hydrolyze a wide range of pyrethroid pesticides. The crystal structures of PytH are solved in this study. This showed that PytH belongs to the α/β-hydrolase fold proteins with typical catalytic Ser-His-Asp triad, though PytH has a low sequence identity (about 20%) with them. The special large hydrophobic binding pocket enabled PytH to bind bigger pyrethroid family substrates. Our structures shed light on the substrate selectivity and the future application of PytH and deepen our understanding of α/β-hydrolase members.

scholarly journals Internal liquid crystal structures in nanocarriers containing drug hydrophobic ion pairs dictate drug release

2021 ◽  
Vol 582 ◽  
pp. 815-824
Author(s):  
Kurt Ristroph ◽  
Malinda Salim ◽  
Brian K. Wilson ◽  
Andrew J. Clulow ◽  
Ben J. Boyd ◽  
...  
Keyword(s):  
Liquid Crystal ◽  
Drug Release ◽  
Crystal Structures ◽  
Ion Pairs

Comparative aspects of glycosyltransferases

2002 ◽  
Vol 69 ◽  
pp. 23-32 ◽  
Author(s):  
Christelle Breton ◽  
Helena Heissigerová ◽  
Charlotte Jeanneau ◽  
Jitka Moravcová ◽  
Anne Imberty
Keyword(s):  
Crystal Structures ◽  
Fold Recognition ◽  
The Other ◽  
Biological Functions ◽  
Direct Role ◽  
Conserved Motifs ◽  
Sequence Identity ◽  
Functional Aspects ◽  
The One ◽  
Limited Sequence

Glycosyltransferases, the enzymes that build oligosaccharides and glycoconjugates, have received much interest in recent years owing to their biological functions and their potential uses in biotechnology. Despite the fact that many glycosyltransferases recognize similar donor or acceptor substrates, there is surprisingly limited sequence identity between different classes. On the one hand, the glycosyltransferases are found in a large number of families, by sequence-based classification. On the other hand, only two structural folds have been identified among the fewer than one dozen glycosyltransferases that have been crystallized at present. Detection of conserved motifs that have a direct role in the functional aspects of glycosyltransferases is one approach for identifying remote similarity. With the availability of more crystal structures, the use of the fold-recognition approach is also very promising.

Mechanistic Investigations on Microbial Type I Terpene Synthases through Site-directed Mutagenesis

Synthesis ◽  
2021 ◽  
Author(s):  
Houchao Xu ◽  
Jeroen Dickschat
Keyword(s):  
Crystal Structures ◽  
Site Directed Mutagenesis ◽  
Terpene Synthase ◽  
Directed Mutagenesis ◽  
Type I ◽  
Terpene Synthases ◽  
Conserved Motifs ◽  
Sequence Identity ◽  
The Past ◽  
Mechanistic Investigations

During the past three decades many terpene synthases have been characterised from all kingdoms of life. The type I of these enzymes from bacteria, fungi and protists commonly exhibit several highly conserved motifs and single residues, and the available crystal structures show a shared -helical fold, while the overall sequence identity is generally low. Several enzymes have been studied by site-directed mutagenesis, giving valuable insights into terpene synthase catalysis and the intriguing mechanisms of terpene synthases. Some mutants are also preparatively useful and give higher yields than the wildtype or a different product that is otherwise difficult to access. The accumulated knowledge obtained from these studies is presented and discussed in this review.

scholarly journals Archaeal actin from a hyperthermophile forms a single-stranded filament

2015 ◽  
Vol 112 (30) ◽  
pp. 9340-9345 ◽  
Author(s):  
Tatjana Braun ◽  
Albina Orlova ◽  
Karin Valegård ◽  
Ann-Christin Lindås ◽  
Gunnar F. Schröder ◽  
...  
Keyword(s):  
Actin Cytoskeleton ◽  
Crystal Structures ◽  
Actin Filaments ◽  
Phylogenetic Analyses ◽  
Atomic Resolution ◽  
Electron Cryomicroscopy ◽  
Large Variability ◽  
Sequence Identity ◽  
Subunit Interface ◽  
Large Insertion

The prokaryotic origins of the actin cytoskeleton have been firmly established, but it has become clear that the bacterial actins form a wide variety of different filaments, different both from each other and from eukaryotic F-actin. We have used electron cryomicroscopy (cryo-EM) to examine the filaments formed by the protein crenactin (a crenarchaeal actin) from Pyrobaculum calidifontis, an organism that grows optimally at 90 °C. Although this protein only has ∼20% sequence identity with eukaryotic actin, phylogenetic analyses have placed it much closer to eukaryotic actin than any of the bacterial homologs. It has been assumed that the crenactin filament is double-stranded, like F-actin, in part because it would be hard to imagine how a single-stranded filament would be stable at such high temperatures. We show that not only is the crenactin filament single-stranded, but that it is remarkably similar to each of the two strands in F-actin. A large insertion in the crenactin sequence would prevent the formation of an F-actin-like double-stranded filament. Further, analysis of two existing crystal structures reveals six different subunit–subunit interfaces that are filament-like, but each is different from the others in terms of significant rotations. This variability in the subunit–subunit interface, seen at atomic resolution in crystals, can explain the large variability in the crenactin filaments observed by cryo-EM and helps to explain the variability in twist that has been observed for eukaryotic actin filaments.

Crystal structures of an archaeal thymidylate kinase from Sulfolobus tokodaii provide insights into the role of a conserved active site Arginine residue

2017 ◽  
Vol 197 (3) ◽  
pp. 236-249 ◽  
Author(s):  
Ansuman Biswas ◽  
Arpit Shukla ◽  
R.S.K. Vijayan ◽  
Jeyaraman Jeyakanthan ◽  
Kanagaraj Sekar
Keyword(s):  
Crystal Structures ◽  
Active Site ◽  
Arginine Residue ◽  
Thymidylate Kinase ◽  
Sulfolobus Tokodaii
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