Product formation controlled by substrate dynamics in leukotriene A4 hydrolase

Stsiapanava, A.; Tholander, Fredrik; Kumar, Ramakrishnan B.; Qureshi, Abdul Aziz; Niegowski, Damian; Hasan, Mahmudul; Thunnissen, Marjolein M.G.M.; Haeggström, Jesper Z.; Rinaldo-Matthis, Agnes

doi:10.1016/j.bbapap.2013.12.003

Cited by 8 publications

(16 citation statements)

References 126 publications

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“…This conclusion is consistent with the previously reported formation of ALOX5 products (5-HETE, LTB4, LTC4) by frog leukocytes [170]. Recently, the LTA4H of the African claw toad (Xenopus laevis) was cloned and the enzyme was shown to convert LTA4 to LTB4 and D(6)-trans-D(8)-cis-LTB4 [171]. This data suggest that amphibia apparently had a functional leukotriene B4 synthesizing cascade.…”

Section: Speciessupporting

confidence: 91%

Evolutionary aspects of lipoxygenases and genetic diversity of human leukotriene signaling

Horn

Adel

Schumann

et al. 2015

Progress in Lipid Research

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Leukotrienes are pro-inflammatory lipid mediators, which are biosynthesized via the lipoxygenase pathway of the arachidonic acid cascade. Lipoxygenases form a family of lipid peroxidizing enzymes and human lipoxygenase isoforms have been implicated in the pathogenesis of inflammatory, hyperproliferative (cancer) and neurodegenerative diseases. Lipoxygenases are not restricted to humans but also occur in a large number of pro- and eucaryotic organisms. Lipoxygenase-like sequences have been identified in the three domains of life (bacteria, archaea, eucarya) but because of lacking functional data the occurrence of catalytically active lipoxygenases in archaea still remains an open question. Although the physiological and/or pathophysiological functions of various lipoxygenase isoforms have been studied throughout the last three decades there is no unifying concept for the biological importance of these enzymes. In this review we are summarizing the current knowledge on the distribution of lipoxygenases in living single and multicellular organisms with particular emphasis to higher vertebrates and will also focus on the genetic diversity of enzymes and receptors involved in human leukotriene signaling.

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Section: Speciessupporting

confidence: 91%

Evolutionary aspects of lipoxygenases and genetic diversity of human leukotriene signaling

Horn

Adel

Schumann

et al. 2015

Progress in Lipid Research

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“…This is the case for the X. laevis LTA 4 H that produces this second metabolite [37]. The production of this LTB 4 isomeric compound is abolished by the corresponding F 375 Y mutation (human LTA 4 H, Y 378 ; Ap-B, Y 409 ) [38]. A role for the Y 375 hydroxyl group in the stabilization by a hydrogen bond of the Y 380 catalytic residue (Ap-B, Y 414 ) was thus proposed [38].…”

Section: Tyrosine 409mentioning

confidence: 99%

“…The production of this LTB 4 isomeric compound is abolished by the corresponding F 375 Y mutation (human LTA 4 H, Y 378 ; Ap-B, Y 409 ) [38]. A role for the Y 375 hydroxyl group in the stabilization by a hydrogen bond of the Y 380 catalytic residue (Ap-B, Y 414 ) was thus proposed [38]. From all of these observations, a question arises and for which a response will be probably brought in the future: Is the hydroxyl group of the tyrosine residue (Ap-B, Y 409 ) necessary for the hydrolysis of peptides by the M1 aminopeptidases with three structural domains?…”

Section: Tyrosine 409mentioning

confidence: 99%

The M1 family of vertebrate aminopeptidases: Role of evolutionarily conserved tyrosines in the enzymatic mechanism of aminopeptidase B

et al. 2015

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Aminopeptidase B (Ap-B), a member of the M1 family of Zn(2+)-aminopeptidases, removes basic residues at the NH2-terminus of peptides and is involved in the in vivo proteolytic processing of miniglucagon and cholecystokinin-8. M1 enzymes hydrolyze numerous different peptides and are implicated in many physiological functions. As these enzymes have similar catalytic mechanisms, their respective substrate specificity and/or catalytic efficiency must be based on subtle structural differences at or near the catalytic site. This leads to the hypothesis that each primary structure contains a consensus structural template, strictly necessary for aminopeptidase activity, and a specific amino acid environment localized in or outside the catalytic pocket that finely tunes the substrate specificity and catalytic efficiency of each enzyme. A multiple sequence alignment of M1 peptidases from vertebrates allowed to identify conserved tyrosine amino acids, which are members of this catalytic backbone. In the present work, site-directed mutagenesis and 3D molecular modeling of Ap-B were used to specify the role of four fully (Y281, Y229, Y414, and Y441) and one partially (Y409) conserved residues. Tyrosine to phenylalanine mutations allowed confirming the influence of the hydroxyl groups on the enzyme activity. These groups are implicated in the reaction mechanism (Y414), in substrate specificity and/or catalytic efficiency (Y409), in stabilization of essential amino acids of the active site (Y229, Y409) and potentially in the maintenance of its structural integrity (Y281, Y441). The importance of hydrogen bonds is verified by the Y229H substitution, which preserves the enzyme activity. These data provide new insights into the catalytic mechanism of Ap-B in the M1 family of aminopeptidases.

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“…Interestingly in our study, relaxation of the crystal contacts also produced an increase in size of the S1 substrate pocket that immediately resulted in fluctuations in the position of the Phe ring. Rotation of the Phe ring when bestatin is bound is also not unique to Pf A‐M1, as other crystal structures have identified different positions of the Phe ring . Positioning of the Phe ring relies on π–π stacking in Pf A‐M1 as well as in porcine aminopeptidase N and the human aminopeptidase A .…”

Section: Discussionmentioning

confidence: 98%

“…With the exception of APN, the bestatin‐bound M1 aminopeptidases show a conserved binding mode wherein the backbone hydroxy ketone of bestatin coordinates the active site zinc ion . In APN, it is the terminal carboxylic acid that coordinates the zinc, which results in a completely different binding pose .…”

Section: Discussionmentioning

confidence: 99%

Mapping the Pathway and Dynamics of Bestatin Inhibition of the Plasmodium falciparum M1 Aminopeptidase PfA‐M1

et al. 2018

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The M1 metallo‐aminopeptidase from Plasmodium falciparum, PfA‐M1, is an attractive drug target for the design of new antimalarials. Bestatin, a broad‐spectrum metalloprotease inhibitor, is a moderate inhibitor of PfA‐M1, and has been used to provide structure–activity relationships to inform drug design. The crystal structure of PfA‐M1 with bestatin bound within its active site has been determined; however, dynamics of the inhibitor and the association or dissociation pathway have yet to be characterized. Here we present an all‐atom molecular dynamics study where we have generated a hidden Markov state model from 2.3 μs of molecular dynamics simulation. Our hidden Markov state model identifies five macrostates that clearly show the events involved in bestatin dissociation from the PfA‐M1 active site. The results show for the first time that bestatin can escape the substrate specificity pockets of the enzyme, primarily due to weak interactions within the pockets. Our approach identifies relevant conformational sampling of the inhibitor inside the enzyme and the protein dynamics that could be exploited to produce potent and selective inhibitors that can differentiate between similar members of the M1 aminopeptidase superfamily.

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Product formation controlled by substrate dynamics in leukotriene A4 hydrolase

Cited by 8 publications

References 126 publications

Evolutionary aspects of lipoxygenases and genetic diversity of human leukotriene signaling

Evolutionary aspects of lipoxygenases and genetic diversity of human leukotriene signaling

The M1 family of vertebrate aminopeptidases: Role of evolutionarily conserved tyrosines in the enzymatic mechanism of aminopeptidase B

Mapping the Pathway and Dynamics of Bestatin Inhibition of the Plasmodium falciparum M1 Aminopeptidase PfA‐M1

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