Cofactor assisted gating mechanism in the active site of NADH oxidase from Thermus thermophilus

2006 ◽  
Vol 64 (2) ◽  
pp. 465-476 ◽  
Author(s):  
Jozef Hritz ◽  
Gabriel Žoldák ◽  
Erik Sedlák
Keyword(s):  
Active Site ◽  
Nadh Oxidase ◽  
Thermus Thermophilus ◽  
Gating Mechanism

Active site dynamics in NADH oxidase from Thermus thermophilus studied by NMR spin relaxation

2011 ◽  
Vol 51 (1-2) ◽  
pp. 71-82 ◽  
Author(s):  
Teresa Miletti ◽  
Patrick J. Farber ◽  
Anthony Mittermaier
Keyword(s):  
Spin Relaxation ◽  
Active Site ◽  
Nadh Oxidase ◽  
Thermus Thermophilus ◽  
Nmr Spin Relaxation

Crystal structure of enoyl-CoA hydratase from Thermus thermophilus HB8

2021 ◽  
Vol 77 (5) ◽  
pp. 148-155
Author(s):  
Sivaraman Padavattan ◽  
Sneha Jos ◽  
Hemanga Gogoi ◽  
Bagautdin Bagautdinov
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Thermus Thermophilus ◽  
Tca Cycle ◽  
Significant Shift ◽  
Oxidation Pathway ◽  
Ligand Binding Sites ◽  
Chain Acyl ◽  
Α Helix ◽  
Enoyl Coa Hydratase

Fatty-acid degradation is an oxidative process that involves four enzymatic steps and is referred to as the β-oxidation pathway. During this process, long-chain acyl-CoAs are broken down into acetyl-CoA, which enters the mitochondrial tricarboxylic acid (TCA) cycle, resulting in the production of energy in the form of ATP. Enoyl-CoA hydratase (ECH) catalyzes the second step of the β-oxidation pathway by the syn addition of water to the double bond between C2 and C3 of a 2-trans-enoyl-CoA, resulting in the formation of a 3-hydroxyacyl CoA. Here, the crystal structure of ECH from Thermus thermophilus HB8 (TtECH) is reported at 2.85 Å resolution. TtECH forms a hexamer as a dimer of trimers, and wide clefts are uniquely formed between the two trimers. Although the overall structure of TtECH is similar to that of a hexameric ECH from Rattus norvegicus (RnECH), there is a significant shift in the positions of the helices and loops around the active-site region, which includes the replacement of a longer α3 helix with a shorter α-helix and 310-helix in RnECH. Additionally, one of the catalytic residues of RnECH, Glu144 (numbering based on the RnECH enzyme), is replaced by a glycine in TtECH, while the other catalytic residue Glu164, as well as Ala98 and Gly141 that stabilize the enolate intermediate, is conserved. Their putative ligand-binding sites and active-site residue compositions are dissimilar.

scholarly journals d-Alanine–d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations

2020 ◽  
Vol 295 (23) ◽  
pp. 7894-7904
Author(s):  
Jordan L. Pederick ◽  
Andrew P. Thompson ◽  
Stephen G. Bell ◽  
John B. Bruning
Keyword(s):  
Binding Site ◽  
Active Site ◽  
Drug Target ◽  
Catalytic Mechanism ◽  
Thermus Thermophilus ◽  
Monovalent Cation ◽  
Antibiotic Drug ◽  
Domains Of Life ◽  
Alanine Dipeptide ◽  
Insight Into

The ATP-grasp superfamily of enzymes shares an atypical nucleotide-binding site known as the ATP-grasp fold. These enzymes are involved in many biological pathways in all domains of life. One ATP-grasp enzyme, d-alanine–d-alanine ligase (Ddl), catalyzes ATP-dependent formation of the d-alanyl–d-alanine dipeptide essential for bacterial cell wall biosynthesis and is therefore an important antibiotic drug target. Ddl is activated by the monovalent cation (MVC) K+, but despite its clinical relevance and decades of research, how this activation occurs has not been elucidated. We demonstrate here that activating MVCs bind adjacent to the active site of Ddl from Thermus thermophilus and used a combined biochemical and structural approach to characterize MVC activation. We found that TtDdl is a type II MVC-activated enzyme, retaining activity in the absence of MVCs. However, the efficiency of TtDdl increased ∼20-fold in the presence of activating MVCs, and it was maximally activated by K+ and Rb+ ions. A strict dependence on ionic radius of the MVC was observed, with Li+ and Na+ providing little to no TtDdl activation. To understand the mechanism of MVC activation, we solved crystal structures of TtDdl representing distinct catalytic stages in complex with K+, Rb+, or Cs+. Comparison of these structures with apo TtDdl revealed no evident conformational change on MVC binding. Of note, the identified MVC binding site is structurally conserved within the ATP-grasp superfamily. We propose that MVCs activate Ddl by altering the charge distribution of its active site. These findings provide insight into the catalytic mechanism of ATP-grasp enzymes.

Crystal structure of NADH oxidase from Thermus thermophilus

1995 ◽  
Vol 2 (12) ◽  
pp. 1109-1114 ◽  
Author(s):  
H.J. Hecht ◽  
H. Erdmann ◽  
H.J. Park ◽  
M. Sprinzl ◽  
R.D. Schmid
Keyword(s):  
Crystal Structure ◽  
Nadh Oxidase ◽  
Thermus Thermophilus

Studies of the interaction of NADH oxidase from Thermus thermophilus HB8 with triazine dyes

1994 ◽  
Vol 668 (1) ◽  
pp. 153-164 ◽  
Author(s):  
J. Kirchberger ◽  
H. Erdmann ◽  
H.-J. Hecht ◽  
G. Kopperschläger
Keyword(s):  
Nadh Oxidase ◽  
Thermus Thermophilus ◽  
Thermus Thermophilus Hb8

scholarly journals Dual Role of the Active Site Residues of Thermus thermophilus 3-Isopropylmalate Dehydrogenase: Chemical Catalysis and Domain Closure

Biochemistry ◽  
2016 ◽  
Vol 55 (3) ◽  
pp. 560-574 ◽  
Author(s):  
Éva Gráczer ◽  
Tamás Szimler ◽  
Anita Garamszegi ◽  
Petr V. Konarev ◽  
Anikó Lábas ◽  
...  
Keyword(s):  
Active Site ◽  
Thermus Thermophilus ◽  
Dual Role ◽  
Active Site Residues ◽  
Chemical Catalysis ◽  
Isopropylmalate Dehydrogenase

Alternate pathways for NADH oxidation in Thermus thermophilus using type 2 NADH dehydrogenases

2013 ◽  
Vol 394 (5) ◽  
pp. 667-676 ◽  
Author(s):  
Padmaja Venkatakrishnan ◽  
Andrea M. Lencina ◽  
Lici A. Schurig-Briccio ◽  
Robert B. Gennis
Keyword(s):  
Nadh Dehydrogenase ◽  
Nadh Oxidase ◽  
Thermus Thermophilus ◽  
Biochemical Properties ◽  
Proton Motive Force ◽  
Multiprotein Complex ◽  
Membrane Bound ◽  
Nadh Dehydrogenases ◽  
Single Subunit

Abstract Type 2 NADH dehydrogenase (NDH-2) is a single-subunit membrane-associated flavoenzyme that is part of the respiratory chain of many prokaryotes. The enzyme catalyzes the electron transfer from NADH to quinone but is not directly coupled to the generation of a proton motive force. The purpose of the current work is to compare two different NDH-2s that are encoded in strains of Thermus thermophilus. The aerobic T. thermophilus HB27 strain expresses one NDH-2 that has been previously isolated and characterized. In this work it is shown that a gene, which is misannotated as an NADH oxidase, encodes this enzyme. Unlike HB27, strain NAR1 of T. thermophilus is capable of partial denitrification, and in addition its genome contains the nrcN gene that encodes a second putative NDH-2. Of particular interest is the fact that nrcN is part of an operon (nrcDEFN) that is proposed to encode a protein complex specifically required for nitrate reduction. In this work, the nrcN gene has the activity expected of a NDH-2, and functions independently of other components of the putative Nrc complex. The biochemical properties of the two NDH-2 enzymes are compared. Efforts to demonstrate that NrcN is part of a multiprotein complex were not successful. However, the NrcE protein was expressed in Escherichia coli and shown to be a membrane-bound protein containing heme B.

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