Investigating the Molecular Determinants for Substrate Channeling in BphI–BphJ, an Aldolase–Dehydrogenase Complex from the Polychlorinated Biphenyls Degradation Pathway

Biochemistry ◽  
2011 ◽  
Vol 50 (39) ◽  
pp. 8407-8416 ◽  
Author(s):  
Jason Carere ◽  
Perrin Baker ◽  
Stephen Y. K. Seah
Keyword(s):  
Polychlorinated Biphenyls ◽  
Degradation Pathway ◽  
Substrate Channeling ◽  
Molecular Determinants ◽  
Dehydrogenase Complex

Characterization of an Aldolase−Dehydrogenase Complex That Exhibits Substrate Channeling in the Polychlorinated Biphenyls Degradation Pathway

Biochemistry ◽  
2009 ◽  
Vol 48 (27) ◽  
pp. 6551-6558 ◽  
Author(s):  
Perrin Baker ◽  
Dan Pan ◽  
Jason Carere ◽  
Adam Rossi ◽  
Weijun Wang ◽  
...  
Keyword(s):  
Polychlorinated Biphenyls ◽  
Degradation Pathway ◽  
Substrate Channeling ◽  
Dehydrogenase Complex

scholarly journals Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Nitish Sathyanarayanan ◽  
Giuseppe Cannone ◽  
Lokesh Gakhar ◽  
Nainesh Katagihallimath ◽  
Ramanathan Sowdhamini ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Ring Opening ◽  
Environmental Pollutants ◽  
Degradation Pathway ◽  
Substrate Channeling ◽  
Enzyme Form ◽  
X Ray Scattering ◽  
Hydrophobic Tunnel ◽  
Metabolite Channeling

Abstract Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use of electrostatic highways or pivoting and by conformational changes. The enzyme PaaZ is used by many bacteria to degrade environmental pollutants. PaaZ is a bifunctional enzyme that catalyzes the ring opening of oxepin-CoA and converts it to 3-oxo-5,6-dehydrosuberyl-CoA. Here we report the structures of PaaZ determined by electron cryomicroscopy with and without bound ligands. The structures reveal that three domain-swapped dimers of the enzyme form a trilobed structure. A combination of small-angle X-ray scattering (SAXS), computational studies, mutagenesis and microbial growth experiments suggests that the key intermediate is transferred from one active site to the other by a mechanism of electrostatic pivoting of the CoA moiety, mediated by a set of conserved positively charged residues.

scholarly journals Toward an Understanding Of the Structural and Mechanistic Aspects of Protein-Protein Interactions in 2-Oxo Acid Dehydrogenase Complexes

2021 ◽  
Author(s):  
Natalia S. Nemeria ◽  
Xu Zhang ◽  
Joao Leandro ◽  
Jieyu Zhou ◽  
Luying Yang ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Tca Cycle ◽  
Degradation Pathway ◽  
Protein Protein Interactions ◽  
Acid Dehydrogenase ◽  
The Tca Cycle ◽  
Hybrid Complex ◽  
Key Enzyme ◽  
Lysine Degradation ◽  
Dehydrogenase Complex

The 2-oxoglutarate dehydrogenase complex (OGDHc) is a key enzyme in the TCA cycle and represents one of the major regulators of mitochondrial metabolism through NADH and reactive oxygen species levels. The OGDHc impacts cell metabolic and cell signaling pathways through the coupling of 2-oxoglutarate metabolism to gene transcription related to tumor cell proliferation and aging. DHTKD1 is a gene encoding 2-oxoadipate dehydrogenase (E1a), which functions in the L-lysine degradation pathway. The potentially damaging variants in DHTKD1 have been associated to the (neuro) pathogenesis of several diseases. Evidence was obtained for the formation of a hybrid complex between the OGDHc and E1a, suggesting a potential cross talk between the two metabolic pathways and raising fundamental questions about their assembly. Here we reviewed the recent findings and advances in understanding of protein-protein interactions in OGDHc and 2-oxoadipate dehydrogenase complex (OADHc), an understanding that will create a scaffold to help design approaches to mitigate the effects of diseases associated with dysfunction of the TCA cycle or lysine degradation. A combination of biochemical, biophysical and structural approaches such as chemical cross-linking MS and cryo-EM appears particularly promising to provide vital information for the assembly of 2-oxo acid dehydrogenase complexes, their function and regulation.

The in vitro hydroxylation of 4′-chloro-4-biphenylol by a mushroom tyrosinase preparation

1976 ◽  
Vol 22 (1) ◽  
pp. 104-106 ◽  
Author(s):  
S. Safe ◽  
B. E. Ellis ◽  
O. Hutzinger
Keyword(s):  
Polychlorinated Biphenyls ◽  
Degradation Products ◽  
Degradation Pathway ◽  
Urinary Metabolite ◽  
Mushroom Tyrosinase ◽  
Metabolic Degradation

Incubation of 4′-chloro-4-biphenylol with a mushroom tyrosinase preparation gave the catechol, 4′-chIoro-3,4-biphenyldiol as the sole in vitro metabolite. This compound was identical with the major rat urinary metabolite of 4′-chloro-4-biphenylol and thus confirms the structure assigned to the metabolite. This result also demonstrates a possible degradation pathway of hydroxylated chlorobiphenyls which are themselves the major metabolic degradation products of polychlorinated biphenyls.

scholarly journals Toward an Understanding of the Structural and Mechanistic Aspects of Protein-Protein Interactions in 2-Oxoacid Dehydrogenase Complexes

Life ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 407
Author(s):  
Natalia S. Nemeria ◽  
Xu Zhang ◽  
Joao Leandro ◽  
Jieyu Zhou ◽  
Luying Yang ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Tca Cycle ◽  
Degradation Pathway ◽  
Protein Protein Interactions ◽  
Gene Encoding ◽  
The Tca Cycle ◽  
Hybrid Complex ◽  
Key Enzyme ◽  
Lysine Degradation ◽  
Dehydrogenase Complex

The 2-oxoglutarate dehydrogenase complex (OGDHc) is a key enzyme in the tricarboxylic acid (TCA) cycle and represents one of the major regulators of mitochondrial metabolism through NADH and reactive oxygen species levels. The OGDHc impacts cell metabolic and cell signaling pathways through the coupling of 2-oxoglutarate metabolism to gene transcription related to tumor cell proliferation and aging. DHTKD1 is a gene encoding 2-oxoadipate dehydrogenase (E1a), which functions in the L-lysine degradation pathway. The potentially damaging variants in DHTKD1 have been associated to the (neuro) pathogenesis of several diseases. Evidence was obtained for the formation of a hybrid complex between the OGDHc and E1a, suggesting a potential cross talk between the two metabolic pathways and raising fundamental questions about their assembly. Here we reviewed the recent findings and advances in understanding of protein-protein interactions in OGDHc and 2-oxoadipate dehydrogenase complex (OADHc), an understanding that will create a scaffold to help design approaches to mitigate the effects of diseases associated with dysfunction of the TCA cycle or lysine degradation. A combination of biochemical, biophysical and structural approaches such as chemical cross-linking MS and cryo-EM appears particularly promising to provide vital information for the assembly of 2-oxoacid dehydrogenase complexes, their function and regulation.

scholarly journals Degradation of Polychlorinated Biphenyl Metabolites by Naphthalene-Catabolizing Enzymes

1998 ◽  
Vol 64 (12) ◽  
pp. 4637-4642 ◽  
Author(s):  
Diane Barriault ◽  
Jacinthe Durand ◽  
Halim Maaroufi ◽  
Lindsay D. Eltis ◽  
Michel Sylvestre
Keyword(s):  
Polychlorinated Biphenyls ◽  
Polychlorinated Biphenyl ◽  
Degradation Pathway ◽  
Ring Cleavage ◽  
Catabolic Enzymes ◽  
Naphthalene Degradation

ABSTRACT The ability of the dehydrogenase and ring cleavage dioxygenase of the naphthalene degradation pathway to transform 3,4-dihydroxylated biphenyl metabolites was investigated. 1,2-Dihydro-1,2-dihydroxynaphthalene dehydrogenase was expressed as a histidine-tagged protein. The purified enzyme transformed 2,3-dihydro-2,3-dihydroxybiphenyl, 3,4-dihydro-3,4-dihydroxybiphenyl, and 3,4-dihydro-3,4-dihydroxy-2,2′,5,5′-tetrachlorobiphenyl to 2,3-dihydroxybiphenyl, 3,4-dihydroxybiphenyl (3,4-DHB), and 3,4-dihydroxy-2,2′,5,5′-tetrachlorobiphenyl (3,4-DH-2,2′,5,5′-TCB), respectively. Our data also suggested that purified 1,2-dihydroxynaphthalene dioxygenase catalyzed the metacleavage of 3,4-DHB in both the 2,3 and 4,5 positions. This enzyme cleaved 3,4-DH-2,2′,5,5′-TCB and 3,4-DHB at similar rates. These results demonstrate the utility of the naphthalene catabolic enzymes in expanding the ability of the bph pathway to degrade polychlorinated biphenyls.

Characterization of an Aldolase–Dehydrogenase Complex from the Cholesterol Degradation Pathway ofMycobacterium tuberculosis

Biochemistry ◽  
2013 ◽  
Vol 52 (20) ◽  
pp. 3502-3511 ◽  
Author(s):  
Jason Carere ◽  
Sarah E. McKenna ◽  
Matthew S. Kimber ◽  
Stephen Y. K. Seah
Keyword(s):  
Degradation Pathway ◽  
Ofmycobacterium Tuberculosis ◽  
Dehydrogenase Complex

Detection and mapping of interactions between chromatin and the nuclear envelope in drosophila embryos

1995 ◽  
Vol 53 ◽  
pp. 764-765
Author(s):  
W.F. Marshall ◽  
A.F. Dernburg ◽  
B. Harmon ◽  
J.W. Sedat
Keyword(s):  
Nuclear Envelope ◽  
Chromatin Condensation ◽  
Three Dimensional ◽  
Physiological Role ◽  
Nuclear Surface ◽  
Intact Cells ◽  
Molecular Determinants ◽  
Surface Harmonic ◽  
Drosophila Embryos

Interactions between chromatin and nuclear envelope (NE) have been implicated in chromatin condensation, gene regulation, nuclear reassembly, and organization of chromosomes within the nucleus. To further investigate the physiological role played by such interactions, it will be necessary to determine which loci specifically interact with the nuclear envelope. This will not only facilitate identification of the molecular determinants of this interaction, but will also allow manipulation of the pattern of chromatin-NE interactions to probe possible functions. We have developed a microscopic approach to detect and map chromatin-NE interactions inside intact cells.Fluorescence in situ hybridization (FISH) is used to localize specific chromosomal regions within the nucleus of Drosophila embryos and anti-lamin immunofluorescence is used to detect the nuclear envelope. Widefield deconvolution microscopy is then used to obtain a three-dimensional image of the sample (Fig. 1). The nuclear surface is represented by a surface-harmonic expansion (Fig 2). A statistical test for association of the FISH spot with the surface is then performed.

SAC3B is a target of CML19, the centrin 2 of Arabidopsis thaliana

2020 ◽  
Vol 477 (1) ◽  
pp. 173-189 ◽  
Author(s):  
Marco Pedretti ◽  
Carolina Conter ◽  
Paola Dominici ◽  
Alessandra Astegno
Keyword(s):  
Excision Repair ◽  
Complex Structure ◽  
Binding Motif ◽  
C Terminus ◽  
Repair Protein ◽  
Nucleotide Excision ◽  
Ef Hand ◽  
Molecular Determinants ◽  
Structure In Solution

Arabidopsis centrin 2, also known as calmodulin-like protein 19 (CML19), is a member of the EF-hand superfamily of calcium (Ca2+)-binding proteins. In addition to the notion that CML19 interacts with the nucleotide excision repair protein RAD4, CML19 was suggested to be a component of the transcription export complex 2 (TREX-2) by interacting with SAC3B. However, the molecular determinants of this interaction have remained largely unknown. Herein, we identified a CML19-binding site within the C-terminus of SAC3B and characterized the binding properties of the corresponding 26-residue peptide (SAC3Bp), which exhibits the hydrophobic triad centrin-binding motif in a reversed orientation (I8W4W1). Using a combination of spectroscopic and calorimetric experiments, we shed light on the SAC3Bp–CML19 complex structure in solution. We demonstrated that the peptide interacts not only with Ca2+-saturated CML19, but also with apo-CML19 to form a protein–peptide complex with a 1 : 1 stoichiometry. Both interactions involve hydrophobic and electrostatic contributions and include the burial of Trp residues of SAC3Bp. However, the peptide likely assumes different conformations upon binding to apo-CML19 or Ca2+-CML19. Importantly, the peptide dramatically increases the affinity for Ca2+ of CML19, especially of the C-lobe, suggesting that in vivo the protein would be Ca2+-saturated and bound to SAC3B even at resting Ca2+-levels. Our results, providing direct evidence that Arabidopsis SAC3B is a CML19 target and proposing that CML19 can bind to SAC3B through its C-lobe independent of a Ca2+ stimulus, support a functional role for these proteins in TREX-2 complex and mRNA export.

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