scholarly journals The Crystal Structure of the Rare-Cutting Restriction Enzyme SdaI Reveals Unexpected Domain Architecture

Structure ◽  
2006 ◽  
Vol 14 (9) ◽  
pp. 1389-1400 ◽  
Author(s):  
Giedre Tamulaitiene ◽  
Arturas Jakubauskas ◽  
Claus Urbanke ◽  
Robert Huber ◽  
Saulius Grazulis ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Restriction Enzyme ◽  
Domain Architecture

scholarly journals Crystal Structure ofDeinococcus radioduransRecQ Helicase Catalytic Core Domain: The Interdomain Flexibility

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Sheng-Chia Chen ◽  
Chi-Hung Huang ◽  
Chia Shin Yang ◽  
Tzong-Der Way ◽  
Ming-Chung Chang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Deinococcus Radiodurans ◽  
Domain Architecture ◽  
Genome Integrity ◽  
Catalytic Core Domain ◽  
Catalytic Core ◽  
Core Domain ◽  
Winged Helix ◽  
Dna Helicases ◽  
E Coli

RecQ DNA helicases are key enzymes in the maintenance of genome integrity, and they have functions in DNA replication, recombination, and repair. In contrast to most RecQs, RecQ fromDeinococcus radiodurans(DrRecQ) possesses an unusual domain architecture that is crucial for its remarkable ability to repair DNA. Here, we determined the crystal structures of the DrRecQ helicase catalytic core and its ADP-bound form, revealing interdomain flexibility in its first RecA-like and winged-helix (WH) domains. Additionally, the WH domain of DrRecQ is positioned in a different orientation from that of theE. coliRecQ (EcRecQ). These results suggest that the orientation of the protein during DNA-binding is significantly different when comparing DrRecQ and EcRecQ.

scholarly journals Crystal structure of JHP933 from Helicobacter pylori J99

2014 ◽  
Vol 70 (a1) ◽  
pp. C823-C823
Author(s):  
Sang Jae Lee ◽  
Ji Young Yoon ◽  
Bong-Jin Lee ◽  
Se Won Suh
Keyword(s):  
Crystal Structure ◽  
Helicobacter Pylori ◽  
Peptic Ulcer ◽  
Functional Characterization ◽  
Domain Architecture ◽  
Structural Similarity ◽  
Terminal Domain ◽  
Plasticity Region ◽  
H Pylori ◽  
And Function

Helicobacter pylori infection is the main cause of chronic gastritis, gastric mucosal atrophy, peptic ulcer, and some forms of gastric cancer. There has been considerable interest in strain-specific genes found outside of the cag pathogenicity island, especially genes in the plasticity regions of H. pylori. In H. pylori strain J99, the plasticity region contains 48 genes ranging from jhp0914 to jhp0961. Because little is known about many of these genes in the plasticity region, further studies are necessary to elucidate their roles in H. pylori-associated pathogenesis. The JHP933 protein, encoded by the jhp0933 gene in the plasticity region of H. pylori J99, is one of the prevalently expressed proteins in some gastritis and peptic ulcer patients. However, its structure and function remain unknown. Here, we have determined the crystal structure of JHP933, revealing the first two-domain architecture of DUF1814 family. The N-terminal domain has the nucleotidyltransferase fold and the C-terminal domain is a helix bundle. Structural similarity of JHP933 to known nucleotidyltransferases is very remote, suggesting that it may function as a novel nucleotidyltransferase. It is expected that this study will facilitate functional characterization of JHP933 to obtain an insight into its role in pathogenesis by the H. pylori plasticity region.

scholarly journals Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding

2018 ◽  
Vol 293 (39) ◽  
pp. 15043-15054 ◽  
Author(s):  
Pavel Grinkevich ◽  
Dhiraj Sinha ◽  
Iuliia Iermak ◽  
Alena Guzanova ◽  
Marie Weiserova ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Restriction Enzyme ◽  
Type I ◽  
Complex Assembly

Crystal structures of UDP-N-acetylmuramic acid L-alanine ligase (MurC) from Mycobacterium bovis with and without UDP-N-acetylglucosamine

2021 ◽  
Vol 77 (5) ◽  
pp. 618-627
Author(s):  
Pil-Won Seo ◽  
Suk-Youl Park ◽  
Andreas Hofmann ◽  
Jeong-Sun Kim
Keyword(s):  
Crystal Structure ◽  
Cell Wall ◽  
Catalytic Activity ◽  
Amino Acid ◽  
Mycobacterium Bovis ◽  
Domain Architecture ◽  
Binding Domain ◽  
Cross Linking ◽  
Nickel Ion ◽  
Binding Loop

Peptidoglycan comprises repeating units of N-acetylmuramic acid, N-acetylglucosamine and short cross-linking peptides. After the conversion of UDP-N-acetylglucosamine (UNAG) to UDP-N-acetylmuramic acid (UNAM) by the MurA and MurB enzymes, an amino acid is added to UNAM by UDP-N-acetylmuramic acid L-alanine ligase (MurC). As peptidoglycan is an essential component of the bacterial cell wall, the enzymes involved in its biosynthesis represent promising targets for the development of novel antibacterial drugs. Here, the crystal structure of Mycobacterium bovis MurC (MbMurC) is reported, which exhibits a three-domain architecture for the binding of UNAM, ATP and an amino acid as substrates, with a nickel ion at the domain interface. The ATP-binding loop adopts a conformation that is not seen in other MurCs. In the UNAG-bound structure of MbMurC, the substrate mimic interacts with the UDP-binding domain of MbMurC, which does not invoke rearrangement of the three domains. Interestingly, the glycine-rich loop of the UDP-binding domain of MbMurC interacts through hydrogen bonds with the glucose moiety of the ligand, but not with the pyrophosphate moiety. These findings suggest that UNAG analogs might serve as potential candidates for neutralizing the catalytic activity of bacterial MurC.

scholarly journals Crystal Structure of the West Nile Virus Envelope Glycoprotein

2006 ◽  
Vol 80 (23) ◽  
pp. 11467-11474 ◽  
Author(s):  
Grant E. Nybakken ◽  
Christopher A. Nelson ◽  
Beverly R. Chen ◽  
Michael S. Diamond ◽  
Daved H. Fremont
Keyword(s):  
Crystal Structure ◽  
West Nile Virus ◽  
Envelope Glycoprotein ◽  
Domain Architecture ◽  
Conformational Transitions ◽  
Crystalline Lattice ◽  
E Proteins ◽  
Fusion Event ◽  
West Nile ◽  
Fusion Loop

ABSTRACT The envelope glycoprotein (E) of West Nile virus (WNV) undergoes a conformational rearrangement triggered by low pH that results in a class II fusion event required for viral entry. Herein we present the 3.0-Å crystal structure of the ectodomain of WNV E, which reveals insights into the flavivirus life cycle. We found that WNV E adopts a three-domain architecture that is shared by the E proteins from dengue and tick-borne encephalitis viruses and forms a rod-shaped configuration similar to that observed in immature flavivirus particles. Interestingly, the single N-linked glycosylation site on WNV E is displaced by a novel α-helix, which could potentially alter lectin-mediated attachment. The localization of histidines within the hinge regions of E implicates these residues in pH-induced conformational transitions. Most strikingly, the WNV E ectodomain crystallized as a monomer, in contrast to other flavivirus E proteins, which have crystallized as antiparallel dimers. WNV E assembles in a crystalline lattice of perpendicular molecules, with the fusion loop of one E protein buried in a hydrophobic pocket at the DI-DIII interface of another. Dimeric E proteins pack their fusion loops into analogous pockets at the dimer interface. We speculate that E proteins could pivot around the fusion loop-pocket junction, allowing virion conformational transitions while minimizing fusion loop exposure.

scholarly journals Structural insight into the specificity of the B3 DNA-binding domains provided by the co-crystal structure of the C-terminal fragment of BfiI restriction enzyme

2014 ◽  
Vol 42 (6) ◽  
pp. 4113-4122 ◽  
Author(s):  
Dmitrij Golovenko ◽  
Elena Manakova ◽  
Linas Zakrys ◽  
Mindaugas Zaremba ◽  
Giedrius Sasnauskas ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Restriction Enzyme ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Terminal Fragment ◽  
Structural Insight ◽  
Insight Into

scholarly journals Crystal structure of glutathione synthetase at optimal pH: domain architecture and structural similarity with other proteins

1996 ◽  
Vol 9 (12) ◽  
pp. 1083-1092 ◽  
Author(s):  
Keiko Matsuda ◽  
Kenji Mizuguchi ◽  
Takaaki Nishioka ◽  
Hiroaki Kato ◽  
Nobuhiro Go ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Domain Architecture ◽  
Structural Similarity ◽  
Glutathione Synthetase ◽  
Ph Domain ◽  
Optimal Ph

scholarly journals Crystal structure of GCN5 PCAF N-terminal domain reveals atypical ubiquitin ligase structure

2020 ◽  
Vol 295 (43) ◽  
pp. 14630-14639
Author(s):  
Sachiko Toma-Fukai ◽  
Ryota Hibi ◽  
Takao Naganuma ◽  
Mashito Sakai ◽  
Shinya Saijo ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Domain Architecture ◽  
E3 Ligase ◽  
Helical Structure ◽  
New Class ◽  
Ubiquitin E3 Ligase ◽  
Ubiquitin Conjugating Enzyme ◽  
Acetyltransferase Domain ◽  
Insight Into ◽  
Structural Aspects

General control nonderepressible 5 (GCN5, also known as Kat2a) and p300/CBP-associated factor (PCAF, also known as Kat2b) are two homologous acetyltransferases. Both proteins share similar domain architecture consisting of a PCAF N-terminal (PCAF_N) domain, acetyltransferase domain, and a bromodomain. PCAF also acts as a ubiquitin E3 ligase whose activity is attributable to the PCAF_N domain, but its structural aspects are largely unknown. Here, we demonstrated that GCN5 exhibited ubiquitination activity in a similar manner to PCAF and its activity was supported by the ubiquitin-conjugating enzyme UbcH5. Moreover, we determined the crystal structure of the PCAF_N domain at 1.8 Å resolution and found that PCAF_N domain folds into a helical structure with a characteristic binuclear zinc region, which was not predicted from sequence analyses. The zinc region is distinct from known E3 ligase structures, suggesting this region may form a new class of E3 ligase. Our biochemical and structural study provides new insight into not only the functional significance of GCN5 but also into ubiquitin biology.

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