Minrui Fan - Academia.edu (original) (raw)
Papers by Minrui Fan
Nature Communications, 2020
Long-chain alk(a/e)nes represent the major constituents of conventional transportation fuels. Bio... more Long-chain alk(a/e)nes represent the major constituents of conventional transportation fuels. Biosynthesis of alkanes is ubiquitous in many kinds of organisms. Cyanobacteria possess two enzymes, acyl-acyl carrier protein (acyl-ACP) reductase (AAR) and aldehyde-deformylating oxygenase (ADO), which function in a two-step alkane biosynthesis pathway. These two enzymes act in series and possibly form a complex that efficiently converts long chain fatty acyl-ACP/fatty acyl-CoA into hydrocarbon. While the structure of ADO has been previously described, structures of both AAR and AAR–ADO complex have not been solved, preventing deeper understanding of this pathway. Here, we report a ligand-free AAR structure, and three AAR–ADO complex structures in which AARs bind various ligands. Our results reveal the binding pattern of AAR with its substrate/cofactor, and suggest a potential aldehyde-transferring channel from AAR to ADO. Based on our structural and biochemical data, we proposed a model ...
Nature, 2020
Mitochondria take up Ca 2+ through the mitochondrial calcium uniporter complex to regulate energy... more Mitochondria take up Ca 2+ through the mitochondrial calcium uniporter complex to regulate energy production, cytosolic Ca 2+ signaling, and cell death 1,2. In mammals, the uniporter complex (uniplex) contains four core components: the pore-forming MCU, gatekeeper MICU1 and MICU2, and an auxiliary EMRE subunit essential for Ca 2+ transport 3-8. To prevent detrimental Ca 2+ overload, the activity of MCU must be tightly regulated by MICUs, which sense the changes in cytosolic Ca 2+ concentrations to switch MCU on and off 9,10. Here, we report cryo-EM structures of human mitochondrial calcium uniporter holocomplex in inhibited and Ca 2+-activated states. These structures define the architecture of this multi-component Ca 2+ uptake machinery and reveal the gating mechanism by which MICUs control uniporter activity. This work provides a framework for understanding regulated Ca 2+ uptake in mitochondria and lends clues to modulate uniporter activity for treating mitochondrial Ca 2+ overload-related diseases. The uniporter stays quiescent in resting cellular conditions and becomes activated only when local Ca 2+ levels rise above ~1 μM 11,12 This Ca 2+-dependent activation, mediated by a MICU1-MICU2 heterodimer 13,14 , prevents excessive Ca 2+ influx that can increase mitochondrial oxidative stress 15 and trigger apoptosis 1. Mutations that perturb MICU1's
Molecular Plant, 2016
Oxalic acid, the simplest of all dicarboxylic acids, is widely found in all plant species (France... more Oxalic acid, the simplest of all dicarboxylic acids, is widely found in all plant species (Franceschi and Nakata, 2005). Two pathways exist for oxalate degradation in plants: degradation via oxalate oxidase and ATP-and CoA-dependent decarboxylation of oxalate through a poorly studied series of enzymatic reactions (Giovanelli and Tobin, 1961). Oxalyl-CoA synthetase, the enzyme that initiates the second degradation pathway was recently identified in Arabidopsis thaliana as a protein encoded by ACYL-ACTIVATING ENZYME3 (AAE3). It was shown that AAE3dependent degradation of oxalate is important for normal seed development and for defense against oxalate-producing fungal pathogens in Arabidopsis (Foster et al., 2012). In addition, it was shown recently that AAE3 also plays a role in seed development in maize and rice (Wang et al., 2011).
Nature structural & molecular biology, Jan 10, 2015
The photosystem II protein PsbS has an essential role in qE-type nonphotochemical quenching, whic... more The photosystem II protein PsbS has an essential role in qE-type nonphotochemical quenching, which protects plants from photodamage under excess light conditions. qE is initiated by activation of PsbS by low pH, but the mechanism of PsbS action remains elusive. Here we report the low-pH crystal structures of PsbS from spinach in its free form and in complex with the qE inhibitor N,N'-dicyclohexylcarbodiimide (DCCD), revealing that PsbS adopts a unique folding pattern, and, unlike other members of the light-harvesting-complex superfamily, it is a noncanonical pigment-binding protein. Structural and biochemical evidence shows that both active and inactive PsbS form homodimers in the thylakoid membranes, and DCCD binding disrupts the lumenal intermolecular hydrogen bonds of the active PsbS dimer. Activation of PsbS by low pH during qE may involve a conformational change associated with altered lumenal intermolecular interactions of the PsbS dimer.
Acta Crystallographica Section D Biological Crystallography, 2014
Squalene synthase (SQS) is a divalent metal-ion-dependent enzyme that catalyzes the two-step redu... more Squalene synthase (SQS) is a divalent metal-ion-dependent enzyme that catalyzes the two-step reductive `head-to-head' condensation of two molecules of farnesyl pyrophosphate to form squalene using presqualene diphosphate (PSPP) as an intermediate. In this paper, the structures of human SQS and its mutants in complex with several substrate analogues and intermediates coordinated with Mg2+or Mn2+are presented, which stepwise delineate the biosynthetic pathway. Extensive study of the SQS active site has identified several critical residues that are involved in binding reduced nicotinamide dinucleotide phosphate (NADPH). Based on mutagenesis data and a locally closed (JK loop-in) structure observed in thehSQS-(F288L)–PSPP complex, an NADPH-binding model is proposed for SQS. The results identified four major steps (substrate binding, condensation, intermediate formation and translocation) of the ordered sequential mechanisms involved in the `1′–1' isoprenoid biosynthetic pathway....
Nature, Jan 11, 2018
Mitochondrial calcium uptake is critical for regulating ATP production, intracellular calcium sig... more Mitochondrial calcium uptake is critical for regulating ATP production, intracellular calcium signalling, and cell death. This uptake is mediated by a highly selective calcium channel called the mitochondrial calcium uniporter (MCU). Here, we determined the structures of the pore-forming MCU proteins from two fungi by X-ray crystallography and single-particle cryo-electron microscopy. The stoichiometry, overall architecture, and individual subunit structure differed markedly from those described in the recent nuclear magnetic resonance structure of Caenorhabditis elegans MCU. We observed a dimer-of-dimer architecture across species and chemical environments, which was corroborated by biochemical experiments. Structural analyses and functional characterization uncovered the roles of key residues in the pore. These results reveal a new ion channel architecture, provide insights into calcium coordination, selectivity and conduction, and establish a structural framework for understandin...
Nature Communications, 2020
Long-chain alk(a/e)nes represent the major constituents of conventional transportation fuels. Bio... more Long-chain alk(a/e)nes represent the major constituents of conventional transportation fuels. Biosynthesis of alkanes is ubiquitous in many kinds of organisms. Cyanobacteria possess two enzymes, acyl-acyl carrier protein (acyl-ACP) reductase (AAR) and aldehyde-deformylating oxygenase (ADO), which function in a two-step alkane biosynthesis pathway. These two enzymes act in series and possibly form a complex that efficiently converts long chain fatty acyl-ACP/fatty acyl-CoA into hydrocarbon. While the structure of ADO has been previously described, structures of both AAR and AAR–ADO complex have not been solved, preventing deeper understanding of this pathway. Here, we report a ligand-free AAR structure, and three AAR–ADO complex structures in which AARs bind various ligands. Our results reveal the binding pattern of AAR with its substrate/cofactor, and suggest a potential aldehyde-transferring channel from AAR to ADO. Based on our structural and biochemical data, we proposed a model ...
Nature, 2020
Mitochondria take up Ca 2+ through the mitochondrial calcium uniporter complex to regulate energy... more Mitochondria take up Ca 2+ through the mitochondrial calcium uniporter complex to regulate energy production, cytosolic Ca 2+ signaling, and cell death 1,2. In mammals, the uniporter complex (uniplex) contains four core components: the pore-forming MCU, gatekeeper MICU1 and MICU2, and an auxiliary EMRE subunit essential for Ca 2+ transport 3-8. To prevent detrimental Ca 2+ overload, the activity of MCU must be tightly regulated by MICUs, which sense the changes in cytosolic Ca 2+ concentrations to switch MCU on and off 9,10. Here, we report cryo-EM structures of human mitochondrial calcium uniporter holocomplex in inhibited and Ca 2+-activated states. These structures define the architecture of this multi-component Ca 2+ uptake machinery and reveal the gating mechanism by which MICUs control uniporter activity. This work provides a framework for understanding regulated Ca 2+ uptake in mitochondria and lends clues to modulate uniporter activity for treating mitochondrial Ca 2+ overload-related diseases. The uniporter stays quiescent in resting cellular conditions and becomes activated only when local Ca 2+ levels rise above ~1 μM 11,12 This Ca 2+-dependent activation, mediated by a MICU1-MICU2 heterodimer 13,14 , prevents excessive Ca 2+ influx that can increase mitochondrial oxidative stress 15 and trigger apoptosis 1. Mutations that perturb MICU1's
Molecular Plant, 2016
Oxalic acid, the simplest of all dicarboxylic acids, is widely found in all plant species (France... more Oxalic acid, the simplest of all dicarboxylic acids, is widely found in all plant species (Franceschi and Nakata, 2005). Two pathways exist for oxalate degradation in plants: degradation via oxalate oxidase and ATP-and CoA-dependent decarboxylation of oxalate through a poorly studied series of enzymatic reactions (Giovanelli and Tobin, 1961). Oxalyl-CoA synthetase, the enzyme that initiates the second degradation pathway was recently identified in Arabidopsis thaliana as a protein encoded by ACYL-ACTIVATING ENZYME3 (AAE3). It was shown that AAE3dependent degradation of oxalate is important for normal seed development and for defense against oxalate-producing fungal pathogens in Arabidopsis (Foster et al., 2012). In addition, it was shown recently that AAE3 also plays a role in seed development in maize and rice (Wang et al., 2011).
Nature structural & molecular biology, Jan 10, 2015
The photosystem II protein PsbS has an essential role in qE-type nonphotochemical quenching, whic... more The photosystem II protein PsbS has an essential role in qE-type nonphotochemical quenching, which protects plants from photodamage under excess light conditions. qE is initiated by activation of PsbS by low pH, but the mechanism of PsbS action remains elusive. Here we report the low-pH crystal structures of PsbS from spinach in its free form and in complex with the qE inhibitor N,N'-dicyclohexylcarbodiimide (DCCD), revealing that PsbS adopts a unique folding pattern, and, unlike other members of the light-harvesting-complex superfamily, it is a noncanonical pigment-binding protein. Structural and biochemical evidence shows that both active and inactive PsbS form homodimers in the thylakoid membranes, and DCCD binding disrupts the lumenal intermolecular hydrogen bonds of the active PsbS dimer. Activation of PsbS by low pH during qE may involve a conformational change associated with altered lumenal intermolecular interactions of the PsbS dimer.
Acta Crystallographica Section D Biological Crystallography, 2014
Squalene synthase (SQS) is a divalent metal-ion-dependent enzyme that catalyzes the two-step redu... more Squalene synthase (SQS) is a divalent metal-ion-dependent enzyme that catalyzes the two-step reductive `head-to-head' condensation of two molecules of farnesyl pyrophosphate to form squalene using presqualene diphosphate (PSPP) as an intermediate. In this paper, the structures of human SQS and its mutants in complex with several substrate analogues and intermediates coordinated with Mg2+or Mn2+are presented, which stepwise delineate the biosynthetic pathway. Extensive study of the SQS active site has identified several critical residues that are involved in binding reduced nicotinamide dinucleotide phosphate (NADPH). Based on mutagenesis data and a locally closed (JK loop-in) structure observed in thehSQS-(F288L)–PSPP complex, an NADPH-binding model is proposed for SQS. The results identified four major steps (substrate binding, condensation, intermediate formation and translocation) of the ordered sequential mechanisms involved in the `1′–1' isoprenoid biosynthetic pathway....
Nature, Jan 11, 2018
Mitochondrial calcium uptake is critical for regulating ATP production, intracellular calcium sig... more Mitochondrial calcium uptake is critical for regulating ATP production, intracellular calcium signalling, and cell death. This uptake is mediated by a highly selective calcium channel called the mitochondrial calcium uniporter (MCU). Here, we determined the structures of the pore-forming MCU proteins from two fungi by X-ray crystallography and single-particle cryo-electron microscopy. The stoichiometry, overall architecture, and individual subunit structure differed markedly from those described in the recent nuclear magnetic resonance structure of Caenorhabditis elegans MCU. We observed a dimer-of-dimer architecture across species and chemical environments, which was corroborated by biochemical experiments. Structural analyses and functional characterization uncovered the roles of key residues in the pore. These results reveal a new ion channel architecture, provide insights into calcium coordination, selectivity and conduction, and establish a structural framework for understandin...