Crystal structure of LysK, an enzyme catalyzing the last step of lysine biosynthesis in Thermus thermophilus, in complex with lysine: Insight into the mechanism for recognition of the amino-group carrier protein, LysW

2017 ◽  
Vol 491 (2) ◽  
pp. 409-415 ◽  
Author(s):  
Satomi Fujita ◽  
Su-Hee Cho ◽  
Ayako Yoshida ◽  
Fumihito Hasebe ◽  
Takeo Tomita ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Thermus Thermophilus ◽  
Lysine Biosynthesis ◽  
Carrier Protein ◽  
Amino Group ◽  
Insight Into

scholarly journals Structural Insight into Amino Group-carrier Protein-mediated Lysine Biosynthesis

2014 ◽  
Vol 290 (1) ◽  
pp. 435-447 ◽  
Author(s):  
Ayako Yoshida ◽  
Takeo Tomita ◽  
Tsutomu Fujimura ◽  
Chiharu Nishiyama ◽  
Tomohisa Kuzuyama ◽  
...  
Keyword(s):  
Lysine Biosynthesis ◽  
Carrier Protein ◽  
Amino Group ◽  
Structural Insight ◽  
Insight Into

scholarly journals Crystal Structure of Tetrameric Homoisocitrate Dehydrogenase from an Extreme Thermophile, Thermus thermophilus: Involvement of Hydrophobic Dimer-Dimer Interaction in Extremely High Thermotolerance

2005 ◽  
Vol 187 (19) ◽  
pp. 6779-6788 ◽  
Author(s):  
Junichi Miyazaki ◽  
Kuniko Asada ◽  
Shinya Fushinobu ◽  
Tomohisa Kuzuyama ◽  
Makoto Nishiyama
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Thermal Inactivation ◽  
Hydrophobic Interactions ◽  
Substrate Binding ◽  
Thermus Thermophilus ◽  
Lysine Biosynthesis ◽  
Side Chain ◽  
Substrate Binding Site ◽  
Tetramer Formation

ABSTRACT The crystal structure of homoisocitrate dehydrogenase involved in lysine biosynthesis from Thermus thermophilus (TtHICDH) was determined at 1.85-Å resolution. Arg85, which was shown to be a determinant for substrate specificity in our previous study, is positioned close to the putative substrate binding site and interacts with Glu122. Glu122 is highly conserved in the equivalent position in the primary sequence of ICDH and archaeal 3-isopropylmalate dehydrogenase (IPMDH) but interacts with main- and side-chain atoms in the same domain in those paralogs. In addition, a conserved Tyr residue (Tyr125 in TtHICDH) which extends its side chain toward a substrate and thus has a catalytic function in the related β-decarboxylating dehydrogenases, is flipped out of the substrate-binding site. These results suggest the possibility that the conformation of the region containing Glu122-Tyr125 is changed upon substrate binding in TtHICDH. The crystal structure of TtHICDH also reveals that the arm region is involved in tetramer formation via hydrophobic interactions and might be responsible for the high thermotolerance. Mutation of Val135, located in the dimer-dimer interface and involved in the hydrophobic interaction, to Met alters the enzyme to a dimer (probably due to steric perturbation) and markedly decreases the thermal inactivation temperature. Both the crystal structure and the mutation analysis indicate that tetramer formation is involved in the extremely high thermotolerance of TtHICDH.

Crystal Structure of a Lysine Biosynthesis Enzyme, LysX, from Thermus thermophilus HB8

2003 ◽  
Vol 332 (3) ◽  
pp. 729-740 ◽  
Author(s):  
Hiroaki Sakai ◽  
Marina N. Vassylyeva ◽  
Takanori Matsuura ◽  
Shun-ichi Sekine ◽  
Kazumi Gotoh ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Thermus Thermophilus ◽  
Lysine Biosynthesis ◽  
Thermus Thermophilus Hb8

scholarly journals Functional and Evolutionary Relationship between Arginine Biosynthesis and Prokaryotic Lysine Biosynthesis through α-Aminoadipate

2001 ◽  
Vol 183 (17) ◽  
pp. 5067-5073 ◽  
Author(s):  
Junichi Miyazaki ◽  
Nobuyuki Kobashi ◽  
Makoto Nishiyama ◽  
Hisakazu Yamane
Keyword(s):  
Gene Cluster ◽  
Thermus Thermophilus ◽  
Evolutionary Relationship ◽  
Biosynthetic Gene Cluster ◽  
Thermophilic Bacterium ◽  
Lysine Biosynthesis ◽  
Amino Group ◽  
Biosynthetic Gene ◽  
Arginine Biosynthesis ◽  
Amino Donor

ABSTRACT Our previous studies revealed that lysine is synthesized through α-aminoadipate in an extremely thermophilic bacterium, Thermus thermophilus HB27. Sequence analysis of a gene cluster involved in the lysine biosynthesis of this microorganism suggested that the conversion from α-aminoadipate to lysine proceeds in a way similar to that of arginine biosynthesis. In the present study, we cloned anargD homolog of T. thermophilus HB27 which was not included in the previously cloned lysine biosynthetic gene cluster and determined the nucleotide sequence. A knockout of theargD-like gene, now termed lysJ, inT. thermophilus HB27 showed that this gene is essential for lysine biosynthesis in this bacterium. The lysJ gene was cloned into a plasmid and overexpressed in Escherichia coli, and the LysJ protein was purified to homogeneity. When the catalytic activity of LysJ was analyzed in a reverse reaction in the putative pathway, LysJ was found to transfer the ɛ-amino group ofN 2-acetyllysine, a putative intermediate in lysine biosynthesis, to 2-oxoglutarate. WhenN 2-acetylornithine, a substrate for arginine biosynthesis, was used as the substrate for the reaction, LysJ transferred the δ-amino group ofN 2-acetylornithine to 2-oxoglutarate 16 times more efficiently than whenN 2-acetyllysine was the amino donor. All these results suggest that lysine biosynthesis in T. thermophilus HB27 is functionally and evolutionarily related to arginine biosynthesis.

scholarly journals Correction to Crystal Structure of α-Galactosidase from Thermus thermophilus: Insight into Hexamer Assembly and Substrate Specificity

2020 ◽  
Vol 68 (30) ◽  
pp. 8091-8091
Author(s):  
Sheng-Chia Chen ◽  
Szu-Pei Wu ◽  
Yu-Yung Chang ◽  
Tzann-Shun Hwang ◽  
Tzong-Huei Lee ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Substrate Specificity ◽  
Thermus Thermophilus ◽  
Insight Into

scholarly journals Structure-based analysis of the molecular interactions between acyltransferase and acyl carrier protein in vicenistatin biosynthesis

2016 ◽  
Vol 113 (7) ◽  
pp. 1802-1807 ◽  
Author(s):  
Akimasa Miyanaga ◽  
Shohei Iwasawa ◽  
Yuji Shinohara ◽  
Fumitaka Kudo ◽  
Tadashi Eguchi
Keyword(s):  
Crystal Structure ◽  
Protein Interactions ◽  
Acyl Carrier Protein ◽  
Complex Structure ◽  
Binding Pocket ◽  
Carrier Protein ◽  
Protein Protein Interactions ◽  
Substrate Binding Pocket ◽  
Insight Into

Acyltransferases (ATs) are key determinants of building block specificity in polyketide biosynthesis. Despite the importance of protein–protein interactions between AT and acyl carrier protein (ACP) during the acyltransfer reaction, the mechanism of ACP recognition by AT is not understood in detail. Herein, we report the crystal structure of AT VinK, which transfers a dipeptide group between two ACPs, VinL and VinP1LdACP, in vicenistatin biosynthesis. The isolated VinK structure showed a unique substrate-binding pocket for the dipeptide group linked to ACP. To gain greater insight into the mechanism of ACP recognition, we attempted to crystallize the VinK–ACP complexes. Because transient enzyme–ACP complexes are difficult to crystallize, we developed a covalent cross-linking strategy using a bifunctional maleimide reagent to trap the VinK–ACP complexes, allowing the determination of the crystal structure of the VinK–VinL complex. In the complex structure, Arg-153, Met-206, and Arg-299 of VinK interact with the negatively charged helix II region of VinL. The VinK–VinL complex structure allows, to our knowledge, the first visualization of the interaction between AT and ACP and provides detailed mechanistic insights into ACP recognition by AT.

Crystal Structure of α-Galactosidase from Thermus thermophilus: Insight into Hexamer Assembly and Substrate Specificity

2020 ◽  
Vol 68 (22) ◽  
pp. 6161-6169
Author(s):  
Sheng-Chia Chen ◽  
Szu-Pei Wu ◽  
Yu-Yung Chang ◽  
Tzann-Shun Hwang ◽  
Tzong-Huei Lee ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Substrate Specificity ◽  
Thermus Thermophilus ◽  
Insight Into

Crystal structure of KBSi3O8 isostructural with danburite

1993 ◽  
Vol 57 (386) ◽  
pp. 157-164 ◽  
Author(s):  
Mitsuyoshi Kimata
Keyword(s):  
Crystal Structure ◽  
Direct Method ◽  
Crystal Chemical ◽  
Chemical Formula ◽  
Crystal Chemical Formula ◽  
3 Dimensional ◽  
Tetrahedral Sites ◽  
Structural Types ◽  
Coupled Substitution ◽  
Insight Into

AbstractThe crystal structure of KBSi3O8 (orthorhombic, Pnam, with a = 8.683(1), b = 9.253(1), c = 8.272(1) Å,, V = 664.4(1) Å3, Z = 4) has been determined by the direct method applied to 3- dimensional rcflection data. The structure of a microcrystal with the dimensions 20 × 29 × 37 μm was refined to an unweightcd residual of R = 0.031 using 386 non-zero structure amplitudes. KBSi3O8 adopts a structure essentially different from recdmergneritc NaBSi3O8, with the low albite (NaAlSi3O8) structure, and isotypic with danburite CaB2Si2Os which has the same topology as paracelsian BaAl2Si2O8. The chenfical relationship between this sample and danburitc gives insight into a new coupled substitution; K+ + Si4+ = Ca2+ + B3+ in the extraframework and tetrahedral sites. The present occupancy refinement revealed partial disordering of B and Si atoms which jointly reside in two kinds of general equivalent points, T(1) and T(2) sites. Thus the expanded crystal-chemical formula can be written in the form K(B0.44Si0.56)2(B0.06Si0.94)2O8The systematic trend among crystalline compounds with the M+T3+T4+3O8 formula suggests that they exist in one of four structural types; the feldspar structures with T3+/T4+ ordered and/or disordered forms, and the paracelsian and the hollandite structures.

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