Crystal Structure of Haloalkane Dehalogenase LinB fromSphingomonas paucimobilisUT26 at 0.95 Å Resolution:  Dynamics of Catalytic Residues†,‡

Biochemistry ◽  
2004 ◽  
Vol 43 (4) ◽  
pp. 870-878 ◽  
Author(s):  
Aaron J. Oakley ◽  
Martin Klvaňa ◽  
Michal Otyepka ◽  
Yuji Nagata ◽  
Matthew C. J. Wilce ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Haloalkane Dehalogenase ◽  
Catalytic Residues

X-ray crystal structure of Mycobacterium tuberculosis haloalkane dehalogenase Rv2579

2008 ◽  
Vol 1784 (2) ◽  
pp. 351-362 ◽  
Author(s):  
Pooja A. Mazumdar ◽  
Jordan C. Hulecki ◽  
Maia M. Cherney ◽  
Craig R. Garen ◽  
Michael N.G. James
Keyword(s):  
Crystal Structure ◽  
Mycobacterium Tuberculosis ◽  
Haloalkane Dehalogenase ◽  
X Ray

scholarly journals Reconstruction of Mycobacterial Dehalogenase Rv2579 by Cumulative Mutagenesis of Haloalkane Dehalogenase LinB

2003 ◽  
Vol 69 (4) ◽  
pp. 2349-2355 ◽  
Author(s):  
Yuji Nagata ◽  
Zbyněk Prokop ◽  
Soňa Marvanová ◽  
Jana Sýkorová ◽  
Marta Monincová ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Mycobacterium Tuberculosis ◽  
Amino Acid ◽  
Active Site ◽  
Homology Model ◽  
Protein Family ◽  
Sphingomonas Paucimobilis ◽  
Amino Acid Residues ◽  
Haloalkane Dehalogenase

ABSTRACT The homology model of protein Rv2579 from Mycobacterium tuberculosis H37Rv was compared with the crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26, and this analysis revealed that 6 of 19 amino acid residues which form an active site and entrance tunnel are different in LinB and Rv2579. To characterize the effect of replacement of these six amino acid residues, mutations were introduced cumulatively into the six amino acid residues of LinB. The sixfold mutant, which was supposed to have the active site of Rv2579, exhibited haloalkane dehalogenase activity with the haloalkanes tested, confirming that Rv2579 is a member of the haloalkane dehalogenase protein family.

scholarly journals Structural insights into bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ebru Destan ◽  
Busra Yuksel ◽  
Bradley B. Tolar ◽  
Esra Ayan ◽  
Sam Deutsch ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Energy Efficient ◽  
Bifunctional Enzyme ◽  
Catalytic Residues ◽  
Structural Insights ◽  
Essential Reactions

AbstractThe ammonia-oxidizing thaumarchaeal 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle is one of the most energy-efficient CO2 fixation cycles discovered thus far. The protein encoded by Nmar_1308 (from Nitrosopumilus maritimus SCM1) is a promiscuous enzyme that catalyzes two essential reactions within the thaumarchaeal 3HP/4HB cycle, functioning as both a crotonyl-CoA hydratase (CCAH) and 3-hydroxypropionyl-CoA dehydratase (3HPD). In performing both hydratase and dehydratase activities, Nmar_1308 reduces the total number of enzymes necessary for CO2 fixation in Thaumarchaeota, reducing the overall cost for biosynthesis. Here, we present the first high-resolution crystal structure of this bifunctional enzyme with key catalytic residues in the thaumarchaeal 3HP/4HB pathway.

Crystal Structure of the Haloalkane Dehalogenase fromSphingomonas paucimobilisUT26†,‡

Biochemistry ◽  
2000 ◽  
Vol 39 (46) ◽  
pp. 14082-14086 ◽  
Author(s):  
Jaromír Marek ◽  
Jitka Vévodová ◽  
Ivana Kutá Smatanová ◽  
Yuji Nagata ◽  
L. Anders Svensson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Haloalkane Dehalogenase

scholarly journals Crystal structure of the haloalkane dehalogenase DbjA

2005 ◽  
Vol 61 (a1) ◽  
pp. c193-c193
Author(s):  
Y. Sato ◽  
R. Natsume ◽  
Z. Prokop ◽  
M. Senda ◽  
J. Damborsky ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Haloalkane Dehalogenase

The Crystal Structure of Benzoylformate Decarboxylase at 1.6 Å Resolution:  Diversity of Catalytic Residues in Thiamin Diphosphate-Dependent Enzymes†,‡

Biochemistry ◽  
1998 ◽  
Vol 37 (28) ◽  
pp. 9918-9930 ◽  
Author(s):  
Miriam S. Hasson ◽  
Angelika Muscate ◽  
Michael J. McLeish ◽  
Lena S. Polovnikova ◽  
John A. Gerlt ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Thiamin Diphosphate ◽  
Catalytic Residues ◽  
Benzoylformate Decarboxylase

scholarly journals A Haloalkane Dehalogenase from Saccharomonospora viridis Strain DSM 43017, a Compost Bacterium with Unusual Catalytic Residues, Unique (S)-Enantiopreference, and High Thermostability

2020 ◽  
Vol 86 (17) ◽  
Author(s):  
Klaudia Chmelova ◽  
Eva Sebestova ◽  
Veronika Liskova ◽  
Andy Beier ◽  
David Bednar ◽  
...  
Keyword(s):  
Active Site ◽  
Elevated Temperatures ◽  
Protein Sequences ◽  
Thermophilic Bacterium ◽  
Operational Stability ◽  
Haloalkane Dehalogenase ◽  
Content Type ◽  
Catalytic Residues ◽  
High Thermostability ◽  
Saccharomonospora Viridis

ABSTRACT Haloalkane dehalogenases can cleave a carbon-halogen bond in a broad range of halogenated aliphatic compounds. However, a highly conserved catalytic pentad composed of a nucleophile, a catalytic base, a catalytic acid, and two halide-stabilizing residues is required for their catalytic activity. Only a few family members, e.g., DsaA, DmxA, or DmrB, remain catalytically active while employing a single halide-stabilizing residue. Here, we describe a novel haloalkane dehalogenase, DsvA, from a mildly thermophilic bacterium, Saccharomonospora viridis strain DSM 43017, possessing one canonical halide-stabilizing tryptophan (W125). At the position of the second halide-stabilizing residue, DsvA contains the phenylalanine F165, which cannot stabilize the halogen anion released during the enzymatic reaction by a hydrogen bond. Based on the sequence and structural alignments, we identified a putative second halide-stabilizing tryptophan (W162) located on the same α-helix as F165, but on the opposite side of the active site. The potential involvement of this residue in DsvA catalysis was investigated by the construction and biochemical characterization of the three variants, DsvA01 (F165W), DsvA02 (W162F), and DsvA03 (W162F and F165W). Interestingly, DsvA exhibits a preference for the (S)- over the (R)-enantiomers of β-bromoalkanes, which has not been reported before for any characterized haloalkane dehalogenase. Moreover, DsvA shows remarkable operational stability at elevated temperatures. The present study illustrates that protein sequences possessing an unconventional composition of catalytic residues represent a valuable source of novel biocatalysts. IMPORTANCE The present study describes a novel haloalkane dehalogenase, DsvA, originating from a mildly thermophilic bacterium, Saccharomonospora viridis strain DSM 43017. We report its high thermostability, remarkable operational stability at high temperatures, and an (S)-enantiopreference, which makes this enzyme an attractive biocatalyst for practical applications. Sequence analysis revealed that DsvA possesses an unusual composition of halide-stabilizing tryptophan residues in its active site. We constructed and biochemically characterized two single point mutants and one double point mutant and identified the noncanonical halide-stabilizing residue. Our study underlines the importance of searching for noncanonical catalytic residues in protein sequences.

scholarly journals The Crystal Structure of Nα-p-tosyl-lysyl Chloromethylketone-Bound Oligopeptidase B from Serratia Proteamaculans Revealed a New Type of Inhibitor Binding

Crystals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1438
Author(s):  
Vladimir I. Timofeev ◽  
Dmitry E. Petrenko ◽  
Yulia K. Agapova ◽  
Anna V. Vlaskina ◽  
David M. Karlinsky ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Pocket ◽  
Catalytic Triad ◽  
Inhibitor Binding ◽  
Inhibitor Molecule ◽  
Covalent Bonds ◽  
Catalytic Residues ◽  
Serratia Proteamaculans ◽  
Oligopeptidase B ◽  
New Type

A covalent serine protease inhibitor—Na-p-tosyl-lysyl chloromethylketone (TCK) is a modified lysine residue tosylated at the N-terminus and chloromethylated at the C-terminus, one molecule of which is capable of forming two covalent bonds with both Ser and His catalytic residues, was co-crystallized with modified oligopeptidase B (OpB) from Serratia proteomaculans (PSPmod). The kinetics study, which preceded crystallization, shows that the stoichiometry of TCK-dependent inhibition of PSPmod was 1:2 (protein:inhibitor). The crystal structure of the PSPmod-TCK complex, solved at a resolution of 2.3 Å, confirmed a new type of inhibitor binding. Two TCK molecules were bound to one enzyme molecule: one with the catalytic Ser, the other with the catalytic His. Due to this mode of binding, the intermediate state of PSPmod and the disturbed conformation of the catalytic triad were preserved in the PSPmod-TCK complex. Nevertheless, the analysis of the amino acid surroundings of the inhibitor molecule bound to the catalytic Ser and its comparison with that of antipain-bound OpB from Trypanosoma brucei provided an insight in the structure of the PSPmod substrate-binding pocket. Supposedly, the new type of binding is typical for the interaction of chloromethylketone derivatives with two-domain OpBs. In the open conformational state that these enzymes are assumed in solution, the disordered configuration of the catalytic triad prevents simultaneous interaction of one inhibitor molecule with two catalytic residues.

scholarly journals Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205

2013 ◽  
Vol 195 (11) ◽  
pp. 2642-2651 ◽  
Author(s):  
M. Okai ◽  
J. Ohtsuka ◽  
L. F. Imai ◽  
T. Mase ◽  
R. Moriuchi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Haloalkane Dehalogenase
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