MxaJ structure reveals a periplasmic binding protein‐like architecture with unique secondary structural elements

Choi, Jin Kyeong; Cao, Thinh Phat; Kim, Si Wouk; Lee, Kun Ho; Lee, Sung Haeng

doi:10.1002/prot.25283

Cited by 14 publications

(11 citation statements)

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“…Many experimental studies (Skovran et al 2011; Pol et al 2014; Deng, Ro, and Rosenzweig 2018; Ochsner et al 2019) and one mini-review (Keltjens et al 2014) indicate that most XoxF-based systems are comprised of the core periplasmic MDH XoxF, and homologs of XoxJ (Myung Choi et al 2017) (a periplasmic binding protein of unknown function) and XoxG (Zheng et al 2018) (a periplasmic membrane bound cytochrome specific to XoxF). XoxF3-based systems have not been experimentally studied, but one mini-review identified that a few XoxF3 operons include cytochrome genes (Cox, CtaG) (Keltjens et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Do lanthanide-dependent microbial metabolisms drive the release of REEs from weathered granites?

Voutsinos

West-Roberts

Sachdeva

et al. 2022

Preprint

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Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals is critical for the release of phosphate to the biosphere, yet the microorganisms involved, and the genes required for lanthanide metabolism, are poorly understood. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilization and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found gene clusters implicated in lanthanide-based metabolism of methanol (primarily XoxF3 and XoxF5) are surprisingly common in microbial communities in moderately weathered granite where lanthanide phosphate minerals are dissolving. Notably, XoxF3 systems were found in Verrucomicrobia for the first time, and in Acidobacteria, Gemmatimonadetes, and Alphaproteobacteria. The XoxF-containing gene clusters are shared by diverse Acidobacteria and Gemmatimonadetes, and include conserved hypothetical proteins and transporters not associated with the few well studied XoxF systems. Given that siderophore-like molecules that strongly bind lanthanides may be required to solubilize lanthanide phosphates, it is notable that candidate siderophore biosynthesis systems were most prevalent in bacteria in moderately weathered rock, especially in Acidobacteria with lanthanide-based systems. We conclude that the confluence in the zone of moderate weathering of phosphate mineral dissolution, lanthanide utilisation, and methanol oxidation (thus carbonic acid production) may be important during the conversion of granitic rock to soil.

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Section: Introductionmentioning

confidence: 99%

Do lanthanide-dependent microbial metabolisms drive the release of REEs from weathered granites?

Voutsinos

West-Roberts

Sachdeva

et al. 2022

Preprint

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“…Furthermore, it was found that salt inhibits the initial complex formation and the subsequent electron transfer, and the inhibition is proportional to the ionic strength of the medium [ 6 , 10 ]. These observations suggest a novel role for the other protein components of mox operon, such as MxaJ, MxaR, and MxaS, in aiding the electron transfer between MDH and Cyt c L [ 12 , 13 ], especially in bacteria living in seawater (3.5% NaCl) ( Fig. S1B ) [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

“…These observations suggest a novel role for the other protein components of mox operon, such as MxaJ, MxaR, and MxaS, in aiding the electron transfer between MDH and Cyt c L [ 12 , 13 ], especially in bacteria living in seawater (3.5% NaCl) ( Fig. S1B ) [ 12 ]. It underscores the need for further research in order to understand the strategies adapted by marine bacteria to circumvent the high salinity conditions which have an inhibitory effect on electron transfer, the latter being an essential step in the oxidation of methanol to obtain energy.…”

Section: Introductionmentioning

confidence: 99%

“…The marine bacterium Methylophaga aminisulfidivorans MP T ( Ma MP T ), which was isolated from the sea waters of Mokpo, South Korea, was classified as a neutrophilic, moderately halophilic, and vitamin B12-independent facultative methylotroph [ 14 , 15 ]. We had already reported the structures of the mox operon proteins Ma -MDH [ 16 , 17 ] and Ma -MxaJ [ 12 , 13 ], which are expressed in the periplasmic region of the Ma MP T . We had previously shown that the overall interaction between β-subunits and α-subunits of Ma -MDH was stronger than that of terrestrial homologs, providing the structural integrity to Ma -MDH in aquatic environments [ 16 ].…”

Section: Introductionmentioning

confidence: 99%

“…The novel fold in Ma -MxaJ was shown to contain the ‘bi-lobate’ folding architecture found in periplasmic binding proteins (PDB:5SV6) [ 12 ]. A distinctive structural feature of Ma -MxaJ was the presence of an acidic cavity at the interface of the two domains.…”

Section: Introductionmentioning

confidence: 99%

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Crystal structure of Cytochrome cL from the aquatic methylotrophic bacterium Methylophaga aminisulfidivorans MP^T

Ghosh

Dhanasingh

Ryu

et al. 2020

J. Microbiol. Biotechnol.

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Introduction Methylotrophic bacteria utilize methanol as their single carbon source of energy by oxidizing it to formaldehyde (Fig. 1) [1]. Methylotrophs are of great interest in the study of the biogeochemical cycling of methanol as well as the commercial production of complex polymers such as urea-formaldehyde resin and polyoxymethylene plastics [2]. The oxidation of methanol for energy in methylotrophic bacteria is carried out under the control of the methanol oxidizing (mox) operon, which consists of genes such as mxaF, mxaI, mxaJ, mxaG, mxaR, and mxaS, encoding α-and β-subunits of methanol dehydrogenase (MDH), MxaJ, cytochrome c L (Cytc L), MxaR, and MxaS, respectively (Fig. S1A) [3]. MDH comprises two subunits (α and β) and a cofactor pyrroloquinoline quinone (PQQ), which mobilizes two electrons from methanol, thereby converting it to formaldehyde [4]. The two electrons are subsequently transferred from PQQ of MDH to the heme of cytochrome c L through an unknown mechanism, followed by its sequential transfer to Cytc H , cytochrome c oxidase, and finally to ATP synthase in the cell membrane for the generation of ATP molecules (Fig. S1B) [5-8]. The electron transfer from MDH to Cytc L requires complex formation between these two proteins. Previous studies have proposed an interaction between the basic protein MDH and the acidic protein Cytc L for expedient electron transfer [6, 9, 10]. This complex formation is perplexing since it has never been isolated as a stable complex for crystallization, leading to the unavailability of a structure of the same till date. The docked protein complex [6] showed that the distance between the PQQ in the active site of MDH and the heme of Cytc L was approximately 20 Å, which was beyond the ideal electron jump distance (~14 Å) [11]. Furthermore, it was found that salt inhibits the initial complex formation and the subsequent electron transfer, and the inhibition is Cytochrome c L (Cytc L) is an essential protein in the process of methanol oxidation in methylotrophs. It receives an electron from the pyrroloquinoline quinone (PQQ) cofactor of methanol dehydrogenase (MDH) to produce formaldehyde. The direct electron transfer mechanism between Cytc L and MDH remains unknown due to the lack of structural information. To help gain a better understanding of the mechanism, we determined the first crystal structure of heme c containing Cytc L from the aquatic methylotrophic bacterium Methylophaga aminisulfidivorans MP T at 2.13 Å resolution. The crystal structure of Ma-Cytc L revealed its unique features compared to those of the terrestrial homologues. Apart from Fe in heme, three additional metal ion binding sites for Na + , Ca + , and Fe 2+ were found, wherein the ions mostly formed coordination bonds with the amino acid residues on the loop (G93-Y111) that interacts with heme. Therefore, these ions seemed to enhance the stability of heme insertion by increasing the loop's steadiness. The basic N-terminal end, together with helix α4 and loop (G126 to Y136), contributed positive char...

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Biochemical and Structural Characterization of XoxG and XoxJ and Their Roles in Lanthanide‐Dependent Methanol Dehydrogenase Activity

et al. 2019

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Lanthanide (Ln)‐dependent methanol dehydrogenases (MDHs) have recently been shown to be widespread in methylotrophic bacteria. Along with the core MDH protein, XoxF, these systems contain two other proteins, XoxG (a c‐type cytochrome) and XoxJ (a periplasmic binding protein of unknown function), about which little is known. In this work, we have biochemically and structurally characterized these proteins from the methyltroph Methylobacterium extorquens AM1. In contrast to results obtained in an artificial assay system, assays of XoxFs metallated with LaIII, CeIII, and NdIII using their physiological electron acceptor, XoxG, display Ln‐independent activities, but the Km for XoxG markedly increases from La to Nd. This result suggests that XoxG′s redox properties are tuned specifically for lighter Lns in XoxF, an interpretation supported by the unusually low reduction potential of XoxG (+172 mV). The X‐ray crystal structure of XoxG provides a structural basis for this reduction potential and insight into the XoxG–XoxF interaction. Finally, the X‐ray crystal structure of XoxJ reveals a large hydrophobic cleft and suggests a role in the activation of XoxF. These studies enrich our understanding of the underlying chemical principles that enable the activity of XoxF with multiple lanthanides in vitro and in vivo.

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MxaJ structure reveals a periplasmic binding protein‐like architecture with unique secondary structural elements

Cited by 14 publications

References 28 publications

Do lanthanide-dependent microbial metabolisms drive the release of REEs from weathered granites?

Do lanthanide-dependent microbial metabolisms drive the release of REEs from weathered granites?

Crystal structure of Cytochrome cL from the aquatic methylotrophic bacterium Methylophaga aminisulfidivorans MP^T

Biochemical and Structural Characterization of XoxG and XoxJ and Their Roles in Lanthanide‐Dependent Methanol Dehydrogenase Activity

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MxaJ structure reveals a periplasmic binding protein‐like architecture with unique secondary structural elements

Cited by 14 publications

References 28 publications

Do lanthanide-dependent microbial metabolisms drive the release of REEs from weathered granites?

Do lanthanide-dependent microbial metabolisms drive the release of REEs from weathered granites?

Crystal structure of Cytochrome cL from the aquatic methylotrophic bacterium Methylophaga aminisulfidivorans MPT

Biochemical and Structural Characterization of XoxG and XoxJ and Their Roles in Lanthanide‐Dependent Methanol Dehydrogenase Activity

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Product

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Crystal structure of Cytochrome cL from the aquatic methylotrophic bacterium Methylophaga aminisulfidivorans MP^T