Essential Role of Tyrosine 229 of the Oxaloacetate Decarboxylase β-Subunit in the Energy Coupling Mechanism of the Na+Pump†

Biochemistry ◽  
2000 ◽  
Vol 39 (15) ◽  
pp. 4320-4326 ◽  
Author(s):  
Petra Jockel ◽  
Markus Schmid ◽  
Thomas Choinowski ◽  
Peter Dimroth
2020 ◽  
Vol 21 (22) ◽  
pp. 8789
Author(s):  
Yasuhiro Teranishi ◽  
Hiroshi Kuwahara ◽  
Masaru Ueda ◽  
Tadashi Takemura ◽  
Masanori Kusumoto ◽  
...  

A ceramide deficiency in the stratum corneum (SC) is an essential etiologic factor for the dry and barrier-disrupted skin of patients with atopic dermatitis (AD). Previously, we reported that sphingomyelin (SM) deacylase, which hydrolyzes SM and glucosylceramide at the acyl site to yield their lysoforms sphingosylphosphorylcholine (SPC) and glucosylsphingosine, respectively, instead of ceramide and/or acylceramide, is over-expressed in AD skin and results in a ceramide deficiency. Although the enzymatic properties of SM deacylase have been clarified, the enzyme itself remains unidentified. In this study, we purified and characterized SM deacylase from rat skin. The activities of SM deacylase and acid ceramidase (aCDase) were measured using SM and ceramide as substrates by tandem mass spectrometry by monitoring the production of SPC and sphingosine, respectively. Levels of SM deacylase activity from various rat organs were higher in the order of skin > lung > heart. By successive chromatography using Phenyl-5PW, Rotofor, SP-Sepharose, Superdex 200 and Shodex RP18-415, SM deacylase was purified to homogeneity with a single band of an apparent molecular mass of 43 kDa with an enrichment of > 14,000-fold. Analysis by MALDI-TOF MS/MS using a protein spot with SM deacylase activity separated by 2D-SDS-PAGE allowed its amino acid sequence to be determined and identified as the β-subunit of aCDase, which consists of α- and β-subunits linked by amino bonds and a single S-S bond. Western blotting of samples treated with 2-mercaptoethanol revealed that, whereas recombinant human aCDase was recognized by antibodies to the α-subunit at ~56 kDa and ~13 kDa and the β-subunit at ~43 kDa, the purified SM deacylase was detectable only by the antibody to the β-subunit at ~43 kDa. Breaking the S-S bond of recombinant human aCDase with dithiothreitol elicited the activity of SM deacylase with ~40 kDa upon gel chromatography. These results provide new insights into the essential role of SM deacylase expressed as an aCDase-degrading β-subunit that evokes the ceramide deficiency in AD skin.


2018 ◽  
Vol 200 (12) ◽  
Author(s):  
Chunyou Mao ◽  
Yan Zhu ◽  
Pei Lu ◽  
Lipeng Feng ◽  
Shiyun Chen ◽  
...  

ABSTRACT The ω subunit is the smallest subunit of bacterial RNA polymerase (RNAP). Although homologs of ω are essential in both eukaryotes and archaea, this subunit has been known to be dispensable for RNAP in Escherichia coli and in other bacteria. In this study, we characterized an indispensable role of the ω subunit in Mycobacterium tuberculosis . Unlike the well-studied E. coli RNAP, the M. tuberculosis RNAP core enzyme cannot be functionally assembled in the absence of the ω subunit. Importantly, substitution of M. tuberculosis ω with ω subunits from E. coli or Thermus thermophilus cannot restore the assembly of M. tuberculosis RNAP. Furthermore, by replacing different regions in M. tuberculosis ω with the corresponding regions from E. coli ω, we found a nonconserved loop region in M. tuberculosis ω essential for its function in RNAP assembly. From RNAP structures, we noticed that the location of the C-terminal region of the β′ subunit (β′CTD) in M. tuberculosis RNAP but not in E. coli or T. thermophilus RNAP is close to the ω loop region. Deletion of this β′CTD in M. tuberculosis RNAP destabilized the binding of M. tuberculosis ω on RNAP and compromised M. tuberculosis core assembly, suggesting that these two regions may function together to play a role in ω-dependent RNAP assembly in M. tuberculosis . Sequence alignment of the ω loop and the β′CTD regions suggests that the essential role of ω is probably restricted to mycobacteria. Together, our study characterized an essential role of M. tuberculosis ω and highlighted the importance of the ω loop region in M. tuberculosis RNAP assembly. IMPORTANCE DNA-dependent RNA polymerase (RNAP), which consists of a multisubunit core enzyme (α 2 ββ′ω) and a dissociable σ subunit, is the only enzyme in charge of transcription in bacteria. As the smallest subunit, the roles of ω remain the least well studied. In Escherichia coli and some other bacteria, the ω subunit is known to be nonessential for RNAP. In this study, we revealed an essential role of the ω subunit for RNAP assembly in the human pathogen Mycobacterium tuberculosis , and a mycobacterium-specific ω loop that plays a role in this function was also characterized. Our study provides fresh insights for further characterizing the roles of bacterial ω subunit.


1998 ◽  
Vol 330 (2) ◽  
pp. 707-712 ◽  
Author(s):  
J. Christian KETCHUM ◽  
Marwan K. AL-SHAWI ◽  
K. Robert NAKAMOTO

We previously demonstrated that the Escherichia coli F0F1-ATP synthase mutation, γM23K, caused increased energy of interaction between γ- and β-subunits which was correlated to inefficient coupling between catalysis and transport [Al-Shawi, Ketchum and Nakamoto (1997) J. Biol. Chem. 272, 2300-2306]. Based on these results and the X-ray crystallographic structure of bovine F1-ATPase [Abrahams, Leslie, Lutter and Walker (1994) Nature (London) 370, 621-628] γM23K is believed to form an ionized hydrogen bond with βGlu-381 in the conserved β380DELSEED386 segment. In this report, we further test the role of γ-β-subunit interactions by introducing a series of substitutions for βGlu-381 and γArg-242, the residue which forms a hydrogen bond with βGlu-381 in the wild-type enzyme. βE381A, D, and Q were able to restore efficient coupling when co-expressed with γM23K. All three mutations reversed the increased transition state thermodynamic parameters for steady state ATP hydrolysis caused by γM23K. βE381K by itself caused inefficient coupling, but opposite from the effect of γM23K, the transition state thermodynamic parameters were lower than wild-type. These results suggest that the βE381K mutation perturbs the γ-β-subunit interaction and the local conformation of the β380DELSEED386 segment in a specific way that disrupts the communication of coupling information between transport and catalysis. βE381A, L, K, and R, and γR242L and E mutations perturbed enzyme assembly and stability to varying degrees. These results provide functional evidence that the β380DELSEED386 segment and its interactions with the γ-subunit are involved in the mechanism of coupling.


Biochemistry ◽  
2000 ◽  
Vol 39 (9) ◽  
pp. 2307-2315 ◽  
Author(s):  
Petra Jockel ◽  
Markus Schmid ◽  
Julia Steuber ◽  
Peter Dimroth

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Etienne Galemou Yoga ◽  
Kristian Parey ◽  
Amina Djurabekova ◽  
Outi Haapanen ◽  
Karin Siegmund ◽  
...  

AbstractRespiratory complex I catalyzes electron transfer from NADH to ubiquinone (Q) coupled to vectorial proton translocation across the inner mitochondrial membrane. Despite recent progress in structure determination of this very large membrane protein complex, the coupling mechanism is a matter of ongoing debate and the function of accessory subunits surrounding the canonical core subunits is essentially unknown. Concerted rearrangements within a cluster of conserved loops of central subunits NDUFS2 (β1-β2S2 loop), ND1 (TMH5-6ND1 loop) and ND3 (TMH1-2ND3 loop) were suggested to be critical for its proton pumping mechanism. Here, we show that stabilization of the TMH1-2ND3 loop by accessory subunit LYRM6 (NDUFA6) is pivotal for energy conversion by mitochondrial complex I. We determined the high-resolution structure of inactive mutant F89ALYRM6 of eukaryotic complex I from the yeast Yarrowia lipolytica and found long-range structural changes affecting the entire loop cluster. In atomistic molecular dynamics simulations of the mutant, we observed conformational transitions in the loop cluster that disrupted a putative pathway for delivery of substrate protons required in Q redox chemistry. Our results elucidate in detail the essential role of accessory subunit LYRM6 for the function of eukaryotic complex I and offer clues on its redox-linked proton pumping mechanism.


Biochemistry ◽  
1999 ◽  
Vol 38 (41) ◽  
pp. 13461-13472 ◽  
Author(s):  
Petra Jockel ◽  
Marco Di Berardino ◽  
Peter Dimroth

2001 ◽  
Vol 1505 (1) ◽  
pp. 1-14 ◽  
Author(s):  
Peter Dimroth ◽  
Petra Jockel ◽  
Markus Schmid

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