Structure of Hydrogenase in Biohydrogen Production Anaerobic Bacteria

2011 ◽  
pp. 251-258 ◽  
Author(s):  
Ming Du ◽  
Lu Zhang
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Catalytic Mechanism ◽  
Anaerobic Bacteria ◽  
Research Direction ◽  
Biohydrogen Production ◽  
Future Research ◽  
Hydrogen Energy ◽  
Industrialization Process ◽  
Catalytic Mechanisms

Hydrogenase plays an important role in the process of biohydrogen production. Hydrogenases have very unique active sites and are classified into three groups according to the metal composition of the active sites: the [Ni-Fe] hydrogenase, [Fe-Fe] hydrogenase, and [Fe-only] hydrogenase. In this paper, the crystal structures and active sites of three kinds of hydrogenases are examined and compared. These enzymes have an unusual structural feature in common. Their similar active site indicates that the catalytic mechanism of hydrogen activation is probably similar. The understanding of the catalytic mechanisms for the three kinds of hydrogenases may help achieve the industrialization process of hydrogen energy production. Moreover, the future research direction about the hydrogenases from auto-aggregative bacteria and the chemical mimic of hydrogenases structure is discussed.

scholarly journals Short hydrogen bonds in the catalytic mechanism of serine proteases

2008 ◽  
Vol 73 (4) ◽  
pp. 393-403 ◽  
Author(s):  
Vladimir Leskovac ◽  
Svetlana Trivic ◽  
Draginja Pericin ◽  
Mira Popovic ◽  
Julijan Kandrac
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Active Site ◽  
Serine Proteases ◽  
Active Sites ◽  
Catalytic Mechanism ◽  
Data Bank ◽  
Ground State Structure ◽  
Low Barrier Hydrogen Bonds ◽  
Short Hydrogen Bonds

The survey of crystallographic data from the Protein Data Bank for 37 structures of trypsin and other serine proteases at a resolution of 0.78-1.28 ? revealed the presence of hydrogen bonds in the active site of the enzymes, which are formed between the catalytic histidine and aspartate residues and are on average 2.7 ? long. This is the typical bond length for normal hydrogen bonds. The geometric properties of the hydrogen bonds in the active site indicate that the H atom is not centered between the heteroatoms of the catalytic histidine and aspartate residues in the active site. Taken together, these findings exclude the possibility that short "low-barrier" hydrogen bonds are formed in the ground state structure of the active sites examined in this work. Some time ago, it was suggested by Cleland that the "low-barrier hydrogen bond" hypothesis is operative in the catalytic mechanism of serine proteases, and requires the presence of short hydrogen bonds around 2.4 ? long in the active site, with the H atom centered between the catalytic heteroatoms. The conclusions drawn from this work do not exclude the validity of the "low-barrier hydrogen bond" hypothesis at all, but they merely do not support it in this particular case, with this particular class of enzymes.

Investigation of the Catalytic Properties of the Dysthrombin, Thrombin Quick

1979 ◽  
Author(s):  
R.A. Henriksen ◽  
W.G. Owen ◽  
M.E. Nesheim ◽  
K.G. Mann
Keyword(s):  
Active Site ◽  
Mayo Clinic ◽  
Active Sites ◽  
Fluorescence Enhancement ◽  
Catalytic Mechanism ◽  
Antithrombin Iii ◽  
Catalytic Properties ◽  
Inhibitor Binding ◽  
Equivalent Number ◽  
Aggregation Of Platelets

Thrombin Quick (TQ) may be isolated following treatment of Prothrombin Quick [Owen, et al, Mayo Clinic Proceedings, 53: 29-33, (1978)] with Taipan venom, phospholipid and Ca2+. The clotting activity of TQ with fibrinogen is 1/200 that of normal thrombin (T) The activation of Factors V and VIII, and the aggregation of platelets by TQ occurs with an effectiveness of about 1/50 that of thrombin. When incubated with antithrombin III, both T and TQ form inhibitor complexes as determined by dodecylsulfate gel electropheresis. Titration of T and TQ with the fluorescent inhibitor dansylarginine-4-ethylpiperidine amide indicates an equivalent number of active sites based on protein absorption at 280 nm. However, the two enzymes may be distinguished by the decreased fluorescence enhancement observed with TQ relative to T, indicating an increased polarity in the inhibitor binding site of TQ. With the substrate benzoylarginine ethylester, TQ has a Km = 4.5 x 10-5M and kcat - 6.93 compared to Km = 4.0 × 10-5M and kcat = 17.7 for T. This indicates that the defect in TQ esterase activity is in the catalytic mechanism itself and not in substrate binding. The rate of inhibition of TQ by diisopropylphosphofluoridate is decreased. Decreased acylation and deacylation rates for TQ relative to T are observed for tydrolysis of the active site titrant 4-methyumbel1 i feryl-p-guanidlnobenzoate.

scholarly journals The Role of Glutathione in the Isomerization of Δ5-Androstene- 3,17-dione Catalyzed by Human Glutathione Transferase A1-1

2001 ◽  
Vol 276 (15) ◽  
pp. 11698-11704 ◽  
Author(s):  
Pär L. Pettersson ◽  
Bengt Mannervik
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Catalytic Mechanism ◽  
Glutathione Transferase ◽  
Ph Dependence ◽  
Enzymatic Catalysis ◽  
Catalytic Efficiency ◽  
Protonated Form ◽  
Hydroxyl Group ◽  
Isomerization Reaction

Human glutathione transferase (GST) A1-1 efficiently catalyzes the isomerization of Δ5-androstene-3,17-dione (AD) into Δ4-androstene-3,17-dione. High activity requires glutathione, but enzymatic catalysis occurs also in the absence of this cofactor. Glutathione alone shows a limited catalytic effect.S-Alkylglutathione derivatives do not promote the reaction, and the pH dependence of the isomerization indicates that the glutathione thiolate serves as a base in the catalytic mechanism. Mutation of the active-site Tyr9into Phe significantly decreases the steady-state kinetic parameters, alters their pH dependence, and increases the pKavalue of the enzyme-bound glutathione thiol. Thus, Tyr9promotes the reaction via its phenolic hydroxyl group in protonated form. GST A2-2 has a catalytic efficiency with AD 100-fold lower than the homologous GST A1-1. Another Alpha class enzyme, GST A4-4, is 1000-fold less active than GST A1-1. The Y9F mutant of GST A1-1 is more efficient than GST A2-2 and GST A4-4, both having a glutathione cofactor and an active-site Tyr9residue. The active sites of GST A2-2 and GST A1-1 differ by only four amino acid residues, suggesting that proper orientation of AD in relation to the thiolate of glutathione is crucial for high catalytic efficiency in the isomerization reaction. The GST A1-1-catalyzed steroid isomerization provides a complement to the previously described isomerase activity of 3β-hydroxysteroid dehydrogenase.

Investigation of the Catalytic Properties of the Dysthrombin, Thrombin Quick

1979 ◽  
Author(s):  
R Henriksen ◽  
W Owen ◽  
M Nesheim ◽  
K Mann
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Fluorescence Enhancement ◽  
Catalytic Mechanism ◽  
Antithrombin Iii ◽  
Catalytic Properties ◽  
Inhibitor Binding ◽  
Equivalent Number ◽  
Hydrolysis Of ◽  
Aggregation Of Platelets

Thrombin Quick (TQ) may be isolated following treatment of Prothrombin Quick [Owen, et al, Mayo Clinic Proceedings, 53: 29-33, (1978)] with Taipan venom, phospholipid and ca2+. The clotting activity of TQ with fibrinogen is 1/200 that of nornar thrombin (T). The activation of Factors V and VIII, and the aggregation of platelets by TQ occurs with an effectiveness of about 1/50 that of thrombin. when incubated with antithrombin III, both T ad TQ fom inhibitor complexes as determined by dodecylsulfate gel electropheresis. Titration of T and TQ with the fluorescent inhibitor dansylarginine-4-ethylpiperidine amide indicates an equivalent number of active sites based on protein absorption at 280 nm. However, the two enzymes may be distinquished by the decreased fluorescence enhancement observed with TQ relative to T, indicating an increased polarity in the inhibitor binding site of TQ. With the substrate benzoylarginine ethylester, TQ has a Km = 4.5 × 10-5M and kcat= 6.93 compared to Km = 4.0 × 10-5M and kcat= 17.7 for T. This indicates that the defect in TQ esterase activity is in the catalytic mechanism itself and not in substrate binding. The rate of inhibition of TQ by diisopropylphosphofluoridate is decreased. Decreased acylation and deacylation rates for TQ relative to T are observed for hydrolysis of the active site titrant 4-methykl-umbelliferyl-p-guanidinobenzoate

Catalytic mechanisms of oxygen-containing groups over vanadium active sites in an Al-MCM-41 framework for production of 2,5-diformylfuran from 5-hydroxymethylfurfural

2020 ◽  
Vol 10 (1) ◽  
pp. 278-290 ◽  
Author(s):  
Li-Juan Liu ◽  
Zhao-Meng Wang ◽  
Ya-Jing Lyu ◽  
Jin-Feng Zhang ◽  
Zhou Huang ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Active Site ◽  
Active Sites ◽  
Hydroxyl Group ◽  
Catalytic Mechanisms ◽  
Mcm 41

In the V-doped Al-MCM-41 framework, the [V-1] active site with a hydroxyl group displays better catalytic activity than the [V-0] active site without a hydroxyl group toward the oxidation of 5-hydroxymethylfurfural to 2,5-diformylfuran.

Dynamic Interconversion of Metal Active Site Ensembles in Zeolite Catalysis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Siddarth H. Krishna ◽  
Casey B. Jones ◽  
Rajamani Gounder
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Heterogeneous Catalysts ◽  
Mean Field ◽  
Future Research ◽  
Annual Review ◽  
Publication Date ◽  
Turnover Rates ◽  
Practical Applications ◽  
Structure And Motion

Catalysis science is founded on understanding the structure, number, and reactivity of active sites. Kinetic models that consider active sites to be static and noninteracting entities are routinely successful in describing the behavior of heterogeneous catalysts. Yet, active site ensembles often restructure in response to their external environment and even during steady-state catalytic turnover, sometimes requiring non-mean-field kinetic treatments to describe distance-dependent interactions among sites. Such behavior is being recognized more frequently in modern catalysis research, with the advent of experimental methods to quantify turnover rates with increasing precision, an expanding arsenal of operando characterization tools, and computational descriptions of atomic structure and motion at chemical potentials and timescales increasingly relevant to reaction conditions. This review focuses on dynamic changes to metal active site ensembles on zeolite supports, which are silica-based crystalline materials substituted with Al that generate binding sites for isolated and low-nuclearity metal site ensembles. Metal sites can become solvated and mobilized during reaction, facilitating interactions among sites that change their nuclearity and function. Such intersite communication can be regulated by the zeolite support, resulting in non-single-site and potentially non-mean-field kinetic behavior arising from mechanisms of catalytic action that combine elements of those canonically associated with homogeneous and heterogeneous catalysis. We discuss recent literature examples that document dynamic active site behavior in metal-zeolites and outline methodologies to identify and interpret such behavior. We conclude with our outlook on future research directions to develop this evolving branch of catalysis science and harness it for practical applications. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 12 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Structure of Allium lachrymatory factor synthase elucidates catalysis on sulfenic acid substrate

2017 ◽  
Author(s):  
Takatoshi Arakawa ◽  
Yuta Sato ◽  
Jumpei Takabe ◽  
Noriya Masamura ◽  
Masahiro Kato ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Active Site ◽  
Active Sites ◽  
Catalytic Mechanism ◽  
Sigmatropic Rearrangement ◽  
Natural Production ◽  
Lachrymatory Factor ◽  
Biological Decomposition ◽  
Key Residues ◽  
Lachrymatory Factor Synthase

AbstractNatural lachrymatory effects are invoked by small volatile S-oxide compounds. They are produced through alkene sulfenic acids by the action of lachrymatory factor synthase (LFS). Here we present the crystal structures of onion LFS (AcLFS) revealed in solute-free and two solute-stabilized forms. Each structure adopts a single seven-stranded helix-grip fold possessing an internal pocket. Mutagenesis analysis localized the active site to a layer near the bottom of the pocket, which is adjacent to the deduced key residues Arg71, Glu88, and Tyr114. Solute molecules visible on the active site have suggested that AcLFS accepts various small alcohol compounds as well as its natural substrate, and they inhibit this substrate according to their chemistry. Structural homologs have been found in the SRPBCC superfamily, and comparison of the active sites has demonstrated that the electrostatic potential unique to AcLFS could work in capturing the substrate in its specific state. Finally, we propose a rational catalytic mechanism based on intramolecular proton shuttling in which the microenvironment of AcLFS can bypass the canonical [1,4]-sigmatropic rearrangement principle established by microwave studies. Beyond revealing how AcLFS generates the lachrymatory compound, this study provides insights into the molecular machinery dealing with highly labile organosulfur species.Significance statementCrushing of onion liberates a volatile compound, syn-propanethial S-oxide (PTSO), which causes lachrymatory effect on humans. We present the crystal structures of onion LFS (AcLFS), the enzyme responsible for natural production of PTSO. AcLFS features a barrel-like fold, and mutagenic and inhibitory analyses revealed that the key residues are present in the central pocket, harboring highly concentrated aromatic residues plus a dyad motif. The architecture of AcLFS is widespread among proteins with various biological functions, such as abscisic acid receptors and polyketide cyclases, and comparisons with these homologs indicate that unique steric and electronic properties maintain the pocket as a reaction compartment. We propose the molecular mechanism behind PTSO generation and shed light on biological decomposition of short-lived sulfur species.

scholarly journals The Reaction Mechanism of Metallo-β-Lactamases Is Tuned by the Conformation of an Active-Site Mobile Loop

2018 ◽  
Vol 63 (1) ◽  
Author(s):  
Antonela R. Palacios ◽  
María F. Mojica ◽  
Estefanía Giannini ◽  
Magdalena A. Taracila ◽  
Christopher R. Bethel ◽  
...  
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Structural Changes ◽  
Catalytic Mechanism ◽  
Multidrug Resistant ◽  
Loop Sequence ◽  
Life Saving ◽  
Life Threatening ◽  
A Minor ◽  
Almost All

ABSTRACTCarbapenems are “last resort” β-lactam antibiotics used to treat serious and life-threatening health care-associated infections caused by multidrug-resistant Gram-negative bacteria. Unfortunately, the worldwide spread of genes coding for carbapenemases among these bacteria is threatening these life-saving drugs. Metallo-β-lactamases (MβLs) are the largest family of carbapenemases. These are Zn(II)-dependent hydrolases that are active against almost all β-lactam antibiotics. Their catalytic mechanism and the features driving substrate specificity have been matter of intense debate. The active sites of MβLs are flanked by two loops, one of which, loop L3, was shown to adopt different conformations upon substrate or inhibitor binding, and thus are expected to play a role in substrate recognition. However, the sequence heterogeneity observed in this loop in different MβLs has limited the generalizations about its role. Here, we report the engineering of different loops within the scaffold of the clinically relevant carbapenemase NDM-1. We found that the loop sequence dictates its conformation in the unbound form of the enzyme, eliciting different degrees of active-site exposure. However, these structural changes have a minor impact on the substrate profile. Instead, we report that the loop conformation determines the protonation rate of key reaction intermediates accumulated during the hydrolysis of different β-lactams in all MβLs. This study demonstrates the existence of a direct link between the conformation of this loop and the mechanistic features of the enzyme, bringing to light an unexplored function of active-site loops on MβLs.

scholarly journals Active Sites in Heterogeneous Catalytic Reaction on Metal and Metal Oxide: Theory and Practice

Catalysts ◽  
2018 ◽  
Vol 8 (10) ◽  
pp. 478 ◽  
Author(s):  
Yanbo Pan ◽  
Xiaochen Shen ◽  
Libo Yao ◽  
Abdulaziz Bentalib ◽  
Zhenmeng Peng
Keyword(s):  
Metal Oxide ◽  
Active Sites ◽  
Research Direction ◽  
Short Review ◽  
Research Field ◽  
Theory And Practice ◽  
Future Research ◽  
Heterogeneous Catalytic ◽  
The Past ◽  
Catalysis Process

Active sites play an essential role in heterogeneous catalysis and largely determine the reaction properties. Yet identification and study of the active sites remain challenging owing to their dynamic behaviors during catalysis process and issues with current characterization techniques. This article provides a short review of research progresses in active sites of metal and metal oxide catalysts, which covers the past achievements, current research status, and perspectives in this research field. In particular, the concepts and theories of active sites are introduced. Major experimental and computational approaches that are used in active site study are summarized, with their applications and limitations being discussed. An outlook of future research direction in both experimental and computational catalysis research is provided.

Active Site Structure in Zeolite-Supported Lean NOx Catalysts

1997 ◽  
Vol 492 ◽  
Author(s):  
Richard J. Blint
Keyword(s):  
Homogeneous Catalysis ◽  
Active Site ◽  
Active Sites ◽  
Catalytic Mechanism ◽  
Copper Ions ◽  
Hydration Shell ◽  
Copper Ion ◽  
Acid Sites ◽  
Reduction Of No ◽  
Dynamics Simulations

AbstractCopper ions exchanged into the zeolite, ZSM-5, are known to catalyze the reduction of NO to N2 in the oxidizing environment of lean automotive exhaust, but do require trace hydrocarbons. The interface of this catalyst provides a locally reducing environment even when the surrounding exhaust has molecular oxygen concentrations as high as 10%. The mechanism of this reduction is still unclear; however, structure calculations of the active sites and dynamics simulations of species diffusion within the zeolite pores provide insight into the mechanism of reduction. One active site is proposed to be Cu++ ionically bound to a bridge oxygen in a nonsymmetric site within a zeolitic pore. Another proposed site has the copper ion centrally (symmetrically) bound within a six member zeolitic ring. Evidence suggests that the copper ions cycle between Cu++ and Cu+ during the reduction of NO to N2. The nonsymmetric copper ions are shown here to be hydrated ions attached to the Brønsted acid sites in the zeolite. The calculations here show a four member, first hydration shell for Cu++ and a first shell of 2–3 oxygens for the Cu+ ion. An examination of the pore size in ZSM-5 indicates sufficient room for a first and second hydration shell for most of the possible acid sites. The conclusion that the copper ions are typically hydrated suggests that the catalytic mechanism may have much in common with homogeneous catalysis which is sometimes termed heterogenized homogeneous catalysis.

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