Crystal structures of the catalytic domain of HIV-1 integrase free and complexed with its metal cofactor: high level of similarity of the active site with other viral integrases 1 1Edited by R. Huber

1998 ◽  
Vol 282 (2) ◽  
pp. 359-368 ◽  
Author(s):  
Sébastien Maignan ◽  
Jean-Pierre Guilloteau ◽  
Qing Zhou-Liu ◽  
Christine Clément-Mella ◽  
Vincent Mikol
Keyword(s):  
Crystal Structures ◽  
Active Site ◽  
Catalytic Domain ◽  
Metal Cofactor ◽  
High Level ◽  
Hiv 1

scholarly journals Crystal Structures of HIV-1 Tat-derived Nonapeptides Tat-(1–9) and Trp2-Tat-(1–9) Bound to the Active Site of Dipeptidyl-peptidase IV (CD26)

2005 ◽  
Vol 280 (15) ◽  
pp. 14911-14917 ◽  
Author(s):  
Wilhelm Andreas Weihofen ◽  
Jianguo Liu ◽  
Werner Reutter ◽  
Wolfram Saenger ◽  
Hua Fan
Keyword(s):  
Crystal Structures ◽  
Active Site ◽  
Dipeptidyl Peptidase ◽  
Dipeptidyl Peptidase Iv ◽  
Hiv 1

scholarly journals Biological and Structural Characterization of Trypanosoma cruzi Phosphodiesterase C and Implications for Design of Parasite Selective Inhibitors

2012 ◽  
Vol 287 (15) ◽  
pp. 11788-11797 ◽  
Author(s):  
Huanchen Wang ◽  
Stefan Kunz ◽  
Gong Chen ◽  
Thomas Seebeck ◽  
Yiqian Wan ◽  
...  
Keyword(s):  
Trypanosoma Cruzi ◽  
Crystal Structures ◽  
Active Site ◽  
Catalytic Domain ◽  
Trypanosoma Evansi ◽  
Active Site Residues ◽  
Dual Specificity ◽  
Pde Inhibitors ◽  
Starting Model

Trypanosoma cruzi phosphodiesterase C (TcrPDEC) is a potential new drug target for the treatment of Chagas disease but has not been well studied. This study reports the enzymatic properties of various kinetoplastid PDECs and the crystal structures of the unliganded TcrPDEC1 catalytic domain and its complex with an inhibitor. Mutations of PDEC during the course of evolution led to inactivation of PDEC in Trypanosoma brucei/Trypanosoma evansi/Trypanosoma congolense, whereas the enzyme is active in all other kinetoplastids. The TcrPDEC1 catalytic domain hydrolyzes both cAMP and cGMP with a Km of 23.8 μm and a kcat of 31 s−1 for cAMP and a Km of 99.1 μm and a kcat of 17 s−1 for cGMP, thus confirming its dual specificity. The crystal structures show that the N-terminal fragment wraps around the TcrPDEC catalytic domain and may thus regulate its enzymatic activity via direct interactions with the active site residues. A PDE5 selective inhibitor that has an IC50 of 230 nm for TcrPDEC1 binds to TcrPDEC1 in an orientation opposite to that of sildenafil. This observation, together with the screen of the inhibitory potency of human PDE inhibitors against TcrPDEC, implies that the scaffold of some human PDE inhibitors might be used as the starting model for design of parasite PDE inhibitors. The structural study also identified a unique parasite pocket that neighbors the active site and may thus be valuable for the design of parasite-specific inhibitors.

Crystal structures of the GH6 Orpinomyces sp. Y102 CelC7 enzyme with exo and endo activity and its complex with cellobiose

2019 ◽  
Vol 75 (12) ◽  
pp. 1138-1147
Author(s):  
Hsiao-Chuan Huang ◽  
Liu-Hong Qi ◽  
Yo-Chia Chen ◽  
Li-Chu Tsai
Keyword(s):  
Enzymatic Hydrolysis ◽  
Crystal Structures ◽  
Active Site ◽  
Binding Sites ◽  
Glycoside Hydrolase ◽  
Catalytic Domain ◽  
Glycoside Hydrolase Family ◽  
Substrate Binding Sites ◽  
Key Residues ◽  
Hydrolase Family

The catalytic domain (residues 128–449) of the Orpinomyces sp. Y102 CelC7 enzyme (Orp CelC7) exhibits cellobiohydrolase and cellotriohydrolase activities. Crystal structures of Orp CelC7 and its cellobiose-bound complex have been solved at resolutions of 1.80 and 2.78 Å, respectively. Cellobiose occupies subsites +1 and +2 within the active site of Orp CelC7 and forms hydrogen bonds to two key residues: Asp248 and Asp409. Furthermore, its substrate-binding sites have both tunnel-like and open-cleft conformations, suggesting that the glycoside hydrolase family 6 (GH6) Orp CelC7 enzyme may perform enzymatic hydrolysis in the same way as endoglucanases and cellobiohydrolases. LC-MS/MS analysis revealed cellobiose (major) and cellotriose (minor) to be the respective products of endo and exo activity of the GH6 Orp CelC7.

scholarly journals Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening

2019 ◽  
Vol 47 (19) ◽  
pp. 10134-10150 ◽  
Author(s):  
George T Lountos ◽  
Xue Zhi Zhao ◽  
Evgeny Kiselev ◽  
Joseph E Tropea ◽  
Danielle Needle ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Small Molecule ◽  
Anticancer Agents ◽  
Active Site ◽  
Catalytic Domain ◽  
Hot Spot ◽  
Alkylating Agents ◽  
Fragment Screening ◽  
Rational Development ◽  
Biochemical Assays

Abstract Tyrosyl DNA-phosphodiesterase I (TDP1) repairs type IB topoisomerase (TOP1) cleavage complexes generated by TOP1 inhibitors commonly used as anticancer agents. TDP1 also removes DNA 3′ end blocking lesions generated by chain-terminating nucleosides and alkylating agents, and base oxidation both in the nuclear and mitochondrial genomes. Combination therapy with TDP1 inhibitors is proposed to synergize with topoisomerase targeting drugs to enhance selectivity against cancer cells exhibiting deficiencies in parallel DNA repair pathways. A crystallographic fragment screening campaign against the catalytic domain of TDP1 was conducted to identify new lead compounds. Crystal structures revealed two fragments that bind to the TDP1 active site and exhibit inhibitory activity against TDP1. These fragments occupy a similar position in the TDP1 active site as seen in prior crystal structures of TDP1 with bound vanadate, a transition state mimic. Using structural insights into fragment binding, several fragment derivatives have been prepared and evaluated in biochemical assays. These results demonstrate that fragment-based methods can be a highly feasible approach toward the discovery of small-molecule chemical scaffolds to target TDP1, and for the first time, we provide co-crystal structures of small molecule inhibitors bound to TDP1, which could serve for the rational development of medicinal TDP1 inhibitors.

A GH13 α-glucosidase from Weissella cibaria uncommonly acts on short-chain maltooligosaccharides

2021 ◽  
Vol 77 (8) ◽  
Author(s):  
Karan Wangpaiboon ◽  
Pasunee Laohawuttichai ◽  
Sun-Yong Kim ◽  
Tomoyuki Mori ◽  
Santhana Nakapong ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Active Site ◽  
Catalytic Domain ◽  
Hydrolytic Activity ◽  
Size Exclusion ◽  
Short Chain ◽  
Glycoside Hydrolase Family ◽  
Enzyme Active Site ◽  
Weissella Cibaria ◽  
Terminal Domain

α-Glucosidase (EC 3.2.1.20) is a carbohydrate-hydrolyzing enzyme which generally cleaves α-1,4-glycosidic bonds of oligosaccharides and starch from the nonreducing ends. In this study, the novel α-glucosidase from Weissella cibaria BBK-1 (WcAG) was biochemically and structurally characterized. WcAG belongs to glycoside hydrolase family 13 (GH13) and to the neopullanase subfamily. It exhibits distinct hydrolytic activity towards the α-1,4 linkages of short-chain oligosaccharides from the reducing end. The enzyme prefers to hydrolyse maltotriose and acarbose, while it cannot hydrolyse cyclic oligosaccharides and polysaccharides. In addition, WcAG can cleave pullulan hydrolysates and strongly exhibits transglycosylation activity in the presence of maltose. Size-exclusion chromatography and X-ray crystal structures revealed that WcAG forms a homodimer in which the N-terminal domain of one monomer is orientated in proximity to the catalytic domain of another, creating the substrate-binding groove. Crystal structures of WcAG in complexes with maltose, maltotriose and acarbose revealed a remarkable enzyme active site with accessible +2, +1 and −1 subsites, along with an Arg–Glu gate (Arg176–Glu296) in front of the active site. The −2 and −3 subsites were blocked by Met119 and Asn120 from the N-terminal domain of a different subunit, resulting in an extremely restricted substrate preference.

scholarly journals Structural Adaptation of Darunavir Analogs Against Primary Resistance Mutations in HIV-1 Protease

2018 ◽  
Author(s):  
Gordon J. Lockbaum ◽  
Florian Leidner ◽  
Linah N. Rusere ◽  
Mina Henes ◽  
Klajdi Kosovrasti ◽  
...  
Keyword(s):  
Protease Inhibitor ◽  
Crystal Structures ◽  
Active Site ◽  
Active Site Residues ◽  
Resistance Mutations ◽  
Structural Adaptation ◽  
Primary Resistance ◽  
Principle Component ◽  
Flap Region ◽  
Hiv 1

AbstractHIV-1 protease is one of the prime targets of agents used in antiretroviral therapy against HIV. However, under selective pressure of protease inhibitors, primary mutations at the active site weaken inhibitor binding to confer resistance. Darunavir (DRV) is the most potent HIV-1 protease inhibitor in clinic; resistance is limited, as DRV fits well within the substrate envelope. Nevertheless, resistance is observed due to hydrophobic changes at residues including I50, V82 and I84 that line the S1/S1’ pocket within the active site. Through enzyme inhibition assays and a series of 12 crystal structures, we interrogated susceptibility of DRV and two potent analogs to primary S1’ mutations. The analogs had modifications at the hydrophobic P1’ moiety to better occupy the unexploited space in the S1’ pocket where the primary mutations were located. Considerable losses of potency were observed against protease variants with I84V and I50V mutations for all three inhibitors. The crystal structures revealed an unexpected conformational change in the flap region of I50V protease bound to the analog with the largest P1’ moiety, indicating interdependency between the S1’ subsite and the flap region. Collective analysis of protease-inhibitor van der Waals (vdW) interactions in the crystal structures using principle component analysis indicated I84V mutation underlying the largest variation in the vdW contacts. Interestingly, the principle components were able to distinguish inhibitor identity and relative potency solely based on vdW interactions of active site residues in the crystal structures. Our results reveal the interplay between inhibitor P1’ moiety and primary S1’ mutations, as well as suggesting a novel method for distinguishing the interdependence of resistance through principle component analyses.

scholarly journals Wild-Type and YMDD Mutant Murine Leukemia Virus Reverse Transcriptases Are Resistant to 2′,3′-Dideoxy-3′-Thiacytidine

2000 ◽  
Vol 74 (14) ◽  
pp. 6669-6674 ◽  
Author(s):  
Elias K. Halvas ◽  
Evguenia S. Svarovskaia ◽  
Eric O. Freed ◽  
Vinay K. Pathak
Keyword(s):  
Active Site ◽  
Murine Leukemia Virus ◽  
Leukemia Virus ◽  
Nucleoside Analogs ◽  
Wild Type ◽  
Reverse Transcriptases ◽  
Ymdd Motif ◽  
High Level ◽  
Hiv 1 ◽  
Murine Leukemia

ABSTRACT The antiretroviral nucleoside analog 2′,3′-dideoxy-3′-thiacytidine (3TC) is a potent inhibitor of wild-type human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT). A methionine-to-valine or methionine-to-isoleucine substitution at residue 184 in the HIV-1 YMDD motif, which is located at the RT active site, leads to a high level of resistance to 3TC. We sought to determine whether 3TC can inhibit the replication of wild-type murine leukemia virus (MLV), which contains V223 at the YVDD active site motif of the MLV RT, and of the V223M, V223I, V223A, and V223S mutant RTs. Surprisingly, the wild type and all four of the V223 mutants of MLV RT were highly resistant to 3TC. These results indicate that determinants outside the YVDD motif of MLV RT confer a high level of resistance to 3TC. Therefore, structural differences among similar RTs might result in widely divergent sensitivities to antiretroviral nucleoside analogs.

scholarly journals Structural comparison of protiated, H/D-exchanged and deuterated human carbonic anhydrase IX

2019 ◽  
Vol 75 (10) ◽  
pp. 895-903 ◽  
Author(s):  
K. Koruza ◽  
B. Lafumat ◽  
M. Nyblom ◽  
B. P. Mahon ◽  
W. Knecht ◽  
...  
Keyword(s):  
Carbonic Anhydrase ◽  
Crystal Structures ◽  
Active Site ◽  
Catalytic Domain ◽  
Crystal Form ◽  
Carbonic Anhydrase Ix ◽  
Structural Comparison ◽  
X Ray ◽  
Ca Ix ◽  
Human Carbonic Anhydrase

Human carbonic anhydrase IX (CA IX) expression is upregulated in hypoxic solid tumours, promoting cell survival and metastasis. This observation has made CA IX a target for the development of CA isoform-selective inhibitors. To enable structural studies of CA IX–inhibitor complexes using X-ray and neutron crystallography, a CA IX surface variant (CA IXSV; the catalytic domain with six surface amino-acid substitutions) has been developed that can be routinely crystallized. Here, the preparation of protiated (H/H), H/D-exchanged (H/D) and deuterated (D/D) CA IXSV for crystallographic studies and their structural comparison are described. Four CA IXSV X-ray crystal structures are compared: two H/H crystal forms, an H/D crystal form and a D/D crystal form. The overall active-site organization in each version is essentially the same, with only minor positional changes in active-site solvent, which may be owing to deuteration and/or resolution differences. Analysis of the crystal contacts and packing reveals different arrangements of CA IXSV compared with previous reports. To our knowledge, this is the first report comparing three different deuterium-labelled crystal structures of the same protein, marking an important step in validating the active-site structure of CA IXSV for neutron protein crystallography.

Sign in / Sign up

Export Citation Format

Share Document