Weimin Gong's research while affiliated with University of Science and Technology of China and other places
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Publications (149)
Melanin-concentrating hormone (MCH) is a 19-amino-acid neuropeptide playing crucial roles in energy homeostasis, sleep, and various physiological processes. It acts through two G protein-coupled receptors, MCHR1 and MCHR2, with MCHR1 being universally present in mammals and a potential target for treating metabolic and mental health conditions. How...
Lysophosphatidylserine (LysoPS) is a naturally occurring lipid mediator involved in various physiological and pathological processes especially those related to the immune system. GPR34, GPR174, and P2Y10 have been identified as the receptors for LysoPS, and its analogues have been developed as agonists or antagonists for these receptors. However,...
L-ergothioneine is widely distributed among various microbes to regulate their physiology and pathogenicity within complex environments. One of the key steps in the ergothioneine-biosynthesis pathway, the C-S bond cleavage reaction, uses the pyridoxal 5′-phosphate dependent C-S lyase to produce the final product L-ergothioneine. Here, we present th...
Melanin-concentrating hormone (MCH) is a 19-amino acid cyclic neuropeptide playing a crucial role in energy homeostasis, sleep, and other physiological functions. In rodents and humans, MCH promotes feeding through the G protein-coupled receptor MCHR1, making it a promising therapeutical target for metabolic disorders. However, mechanisms for ligan...
GPR84 is a unique orphan G protein-coupled receptor (GPCR) that can be activated by endogenous medium-chain fatty acids (MCFAs). The signaling of GPR84 is largely pro-inflammatory, which can augment inflammatory response, and GPR84 also functions as a pro-phagocytic receptor to enhance phagocytic activities of macrophages. In this study, we show th...
Solid-state nuclear magnetic resonance (ssNMR) methods can probe the motions of membrane proteins in liposomes at the atomic level and propel the understanding of biomolecular processes for which static structures cannot provide a satisfactory description. In this work, we report our study on the fluoride channel Fluc-Ec1 in phospholipid bilayers b...
l-Proline hydroxylase is a member of the non-heme Fe²⁺/α-ketoglutarate (AKG)-dependent hydroxylase family that catalyzes the reaction from l-proline to hydroxy-l-proline, which is widely used in drug synthesis, biochemistry, food supplementation and cosmetic industries. Here, the first crystal structure of l-prolinetrans-hydroxylase and its complex...
GPR84 is a unique orphan G protein-coupled receptor (GPCR) that can be activated by endogenous medium-chain fatty acids (MCFAs). The signaling of GPR84 is largely pro-inflammatory, which can augment inflammatory response, and GPR84 also functions as a pro-phagocytic receptor to enhance the phagocytic activities of macrophages. In this study, we fir...
Stress granules (SGs) are cytoplasmic biomolecular condensates containing proteins and RNAs in response to stress. Ras-GTPase–activating protein binding protein 1 (G3BP1) is a core SG protein. Caprin-1 and ubiquitin specific peptidase 10 (USP10) interact with G3BP1, facilitating and suppressing SG formation, respectively. The crystal structures of...
Tuberculosis-causing mycobacteria have thick cell-wall and capsule layers that are formed from complex structures. Protein secretion across these barriers depends on a specialized protein secretion system, but none has been reported. We show that Mycobacterium tuberculosis Rv3705c and its homologous MSMEG_6251 in Mycobacterium smegmatis are tube-fo...
Current resolved structures of GPCRs and G protein complexes provided important insights into G protein activation. However, the binding or dissociation of GPCRs with G protein is instantaneous and highly dynamic in the intracellular environment. The conformational dynamic of G protein still needs to be addressed. In this study, we applied ¹⁹F solu...
To understand how the RuvC catalytic domain of Class 2 Cas proteins cleaves DNA, it will be necessary to elucidate the structures of RuvC-containing Cas complexes in their catalytically competent states. Cas12i2 is a Class 2 type V-I CRISPR-Cas endonuclease that cleaves target dsDNA by an unknown mechanism. Here, we report structures of Cas12i2–crR...
LXYL-P1-2 is one of the few xylosidases that efficiently catalyze the reaction from 7-β-xylosyl-10-deacetyltaxol (XDT) to 10-deacetyltaxol (DT), and is a potential enzyme used in Taxol industrial production. Here we report the crystal structure of LXYL-P1-2 and its XDT binding complex. These structures reveal an enzyme/product complex with the suga...
Photosensitizers, which harness light energy to upgrade weak reductants to strong reductants, are pivotal components of the natural and artificial photosynthesis machineries. However, it has proved difficult to enhance and expand their functions through genetic engineering. Here we report a genetically encoded, 27 kDa photosensitizer protein (PSP),...
Fluorescent proteins (FPs) with emission wavelengths in the far-red and infrared regions of the spectrum provide powerful tools for deep-tissue and super-resolution imaging. The development of red-shifted FPs has evoked widespread interest and continuous engineering efforts. In this article, based on a computational design and genetic code expansio...
The signaling of prostaglandin D2 (PGD2) through G-protein-coupled receptor (GPCR) CRTH2 is a major pathway in type 2 inflammation. Compelling evidence suggests the therapeutic benefits of blocking CRTH2 signaling in many inflammatory disorders. Currently, a number of CRTH2 antagonists are under clinical investigation, and one compound, fevipiprant...
The accurate modification of the tRNAIle anticodon wobble cytosine 34 is critical for AUA decoding in protein synthesis. Archaeal tRNAIle2 cytosine 34 is modified with agmatine in the presence of ATP by TiaS (tRNAIle2 agmatidine synthetase). Yet, no structure of apo-form full length TiaS is available currently. Here, the crystal structures of apo T...
Mutations in TSC1 or TSC2 cause tuberous sclerosis complex (TSC), an autosomal dominant disorder characterized by the occurrence
of benign tumors in various vital organs and tissues. TSC1 and TSC2, the TSC1 and TSC2 gene products, form the TSC protein
complex that senses specific cellular growth conditions to control mTORC1 signaling. TBC1D7 is the...
SUN proteins are the core components of LINC complexes that span across the nuclear envelope for nuclear positioning and migration. SUN proteins contain at least one predicted coiled-coil domain preceding the SUN domain. Here, we found that the two coiled-coil domains (CC1 and CC2) of SUN2 exhibit distinct oligomeric states. CC2 is a monomer in sol...
Tetrapyrroles, including haem and chlorophyll, play vital roles for various biological processes, such as respiration and photosynthesis, and their biosynthesis is critical for virtually all organisms. In photosynthetic organisms, magnesium chelatase (MgCh) catalyses insertion of magnesium into the centre of protoporphyrin IX, the branch-point prec...
Mutations in Fused in sarcoma (FUS) gene cause a subset of familial amyotrophic lateral sclerosis (ALS), a fatal motor neuron degenerative disease. Wild-type FUS is largely localized in the nucleus, but mutant FUS accumulates in the cytoplasm and forms inclusions. It is unclear whether FUS depletion from the nucleus or FUS inclusions in the cytopla...
Electron transfer (ET) is widely used for driving the processes that underlie the chemistry of life. However, our abilities to probe electron transfer mechanisms in proteins and design redox enzymes are limited, due to the lack of methods to site-specifically insert electron acceptors into proteins in vivo. Here we describe the synthesis and geneti...
While nature employs various covalent and non-covalent strategies to modulate tyrosine (Y) redox potential and pKa to optimize enzyme activities, such approaches have not been systematically applied for the design of functional metalloproteins. Through the genetic incorporation of 3-methoxytyrosine (OMeY) into myoglobin, we recapitulated important...
The FAOD/FPOD family of proteins has the potential to be useful for the longterm detection of blood glucose levels in diabetes patients. A bottleneck for this application is to find or engineer a FAOD/FPOD family enzyme that is specifically active towards α-fructosyl peptides but is inactive towards other types of glycated peptides. Here, the cryst...
Adaptations to hypoxia play an important role in Mycobacterium tuberculosis pathogenesis. Rv0324, which contains an HTH DNA-binding domain and a rhodanese domain, is one of the key transcription regulators in response to hypoxia. M. tuberculosis Rv1674c is a homologue of Rv0324. To understand the interdomain interaction and regulation of the HTH do...
Advances in RNA research and RNA nanotechnology depend on the ability to manipulate and probe RNA with high precision through chemical approaches, both in vitro and in mammalian cells. However, covalent RNA labeling methods with scope and versatility comparable to those of current protein labeling strategies are underdeveloped. A method is reported...
Advances in RNA research and RNA nanotechnology depend on the ability to manipulate and probe RNA with high precision through chemical approaches, both in vitro and in mammalian cells. However, covalent RNA labeling methods with scope and versatility comparable to those of current protein labeling strategies are underdeveloped. A method is reported...
Peptide deformylase (PDF) is a prokaryotic enzyme that catalyzes the deformylation of nascent peptides generated during protein synthesis and water molecules play a key role in these hydrolases. Using X-ray absorption near edge spectroscopy (XANES) and ab initio calculations we accurately probe the local atomic environment of the metal ion binding...
Photo-induced electron transfer (PET) is ubiquitous for photosyn-thesis and fluorescent sensor design. However, genetically coded PET sensors are underdeveloped, due to the lack of methods to site-specifically install PET probes on proteins. Here we describe a family of acid and Mn(III) turn-on fluorescent protein (FP) sensors, named iLovU, based o...
Clustered regularly interspaced short palindromic repeats (CRISPR) together with CRISPR-associated (Cas) proteins form the CRISPR/Cas system to defend against foreign nucleic acids of bacterial and archaeal origin. In the I-E subtype CRISPR/Cas system, eleven subunits from five Cas proteins (CasA1B2C6D1E1) assemble along a CRISPR RNA (crRNA) to for...
During translation, elongation factor G (EF-G) catalyzes the translocation of tRNA2-mRNA inside the ribosome. Translocation is coupled to a cycle of conformational rearrangements of the ribosomal machinery, and how EF-G initiates translocation remains unresolved. Here we performed systematic mutagenesis of Escherichia coli EF-G and analyzed inhibit...
The conserved protein Rv3705c from Mycobacterium tuberculosis has been cloned, expressed, purified and crystallized by the sitting-drop vapour-diffusion method using PEG 3350 as a precipitant. The Rv3705c crystals exhibited space group P6122 or P6522, with unit-cell parameters a = b = 198.0, c = 364.1 Å, α = β = 90, γ = 120°, and diffracted to a re...
Cell death and differentiation is a monthly research journal focused on the exciting field of programmed cell death and apoptosis. It provides a single accessible source of information for both scientists and clinicians, keeping them up-to-date with advances in the field. It encompasses programmed cell death, cell death induced by toxic agents, dif...
Significance
The glutamyl-tRNA reductase (GluTR)-catalyzed reduction of glutamyl-tRNA is the rate-limiting and a pivotal regulation step in the tetrapyrrole biosynthetic pathway. In chloroplast-containing photosynthetic organisms, GluTR binding protein (GluBP) is a newly identified spatial regulator that allocates GluTR for synthesis of different t...
The arginyl-tRNA synthetase (ArgRS) catalyzes the esterification reaction between L-arginine and its cognate tRNAArg. Previously reported structures of ArgRS shed considerable light on the tRNA recognition mechanism, while the aspect of amino acid binding in ArgRS remains largely unexplored. Here we report the first crystal structure of E. coli Arg...
The Escherichia coli cyclic AMP receptor protein (CRP) is a prokaryotic global transcription activator protein that controls the expression of many different genes. Wild-type CRP can bind to special DNA sequences in the presence of cAMP. The substitution of Asp53 by His results in the CRP* phenotype, which does not require exogenous cAMP. In the pr...
Arf1 is a member of the Ras superfamily and is involved in COPI vesicle formation. Arf1-GDP can interact with dimeric p23. Here, human Arf1 (residues 18-181) was cloned, expressed and purified in Escherichia coli. For crystallization, Arf1-GDP was mixed with dimeric p23 peptide in a 1:5 molar ratio. Crystals were obtained which diffracted to 2.7 Å...
Two Viruses to Bind
Structural studies of two different H7N9 influenza viruses isolated from humans—A/Shanghai/1/2013 and A/Anhui/1/2013—which have different amino acid sequences in the receptor binding site, provide data indicating that the virus is in transition with respect to host adaptation. The Shanghai virus was one of the first isolated in...
The FANCM/FAAP24 heterodimer has distinct functions in protecting cells from complex DNA lesions such as interstrand crosslinks. These functions rely on the biochemical activity of FANCM/FAAP24 to recognize and bind to damaged DNA or stalled replication forks. However, the DNA-binding activity of this complex was not clearly defined. We investigate...
Plasma makes it safer: A gaseous H2 /O2 plasma reaction has been developed for the safe direct synthesis of H2 O2 . Low electron density favors the generation of H2 O2 by a chain termination path. This plasma method is promising for the direct synthesis of neutral, high concentration (ca. 60 wt %), and high purity (electronic grade) H2 O2 .
An atmospheric pressure AC discharge reactor with nickel (Ni), stainless steel (SS) and copper (Cu) tube electrodes has been systematically studied for ammonia decomposition. Ammonia conversion increased in the following order: Cu < SS < Ni. Conversion induction period was observed for both Ni and SS electrode reactors. The changes of the ammonia c...
Tuberous sclerosis complex is a disease caused by mutations in two tumor-suppressor genes, TSC1 and TSC2. The TSC1 protein, also known as hamartin, has a critical role in controlling mTOR signalling. TSC1 does not bear apparent sequence homology with other proteins. Here we show that the N-terminal half of yeast TSC1 forms a protease-resistant doma...
The flavoenzyme fructosyl peptide oxidase (FPOX) catalyses the oxidative deglycation of fructosyl amino acids or fructosyl dipeptides to produce amino acids, glucosone and hydrogen peroxide. In this study, FPOX protein from Eupenicillium terrenum sp. (EtFPOX) was expressed in Escherichia coli and purified by Ni-affinity and gel-filtration chromatog...
Par-3, the central organizer of the Par-3/Par-6/atyp-ical protein kinase C complex, is a multimodular scaffold protein that is essential for cell polarity establishment and maintenance. The N-terminal domain (NTD) of Par-3 is capable of self-association to form filament-like structures, although the underlying mechanism is poorly understood. Here,...
Plant Deg5 and Deg8 are two members of the HtrA proteases, a family of oligomeric serine endopeptidases that are involved in a variety of protein quality-control processes. These two HtrA proteases are located in the thylakoid lumen and participate in high-light stress responses by collaborating with other chloroplast proteins. Deg5 and Deg8 degrad...
Par-3, the central organizer of the Par-3/Par-6/atypical protein kinase C complex, is a multimodular scaffold protein that is essential for cell polarity establishment and maintenance. The N-terminal domain (NTD) of Par-3 is capable of self-association to form filament-like structures, although the underlying mechanism is poorly understood. Here, w...
Simple and selective: Tyrosine phosphorylation is a pivotal post-translational modification which regulates the enzymatic activity, protein conformation, and protein-protein interactions. The highly efficient genetic incorporation of 3,5-difluorotyrosine (F2Y) in E. coli and the use of F2Y as a 19 F NMR probe for the tyrosine phosphorylation are re...
Strongly adsorbed N atoms inhibit the ammonia decomposition reaction rate. Plasma-driven catalysis can solve this problem and increase the ammonia conversion from 7.8% to 99.9%. (15)NH3 isotope tracing and optical emission spectroscopy show that gas-phase active species (NH3*, NH˙) in the plasma zone facilitate the desorption step by an Eley-Rideal...
The local atomic environment of a cobalt ion bound to the foldings of
the active site of LiPDF (Co-LiPDF) and EcPDF (Co-EcPDF) in a pH 8.0
buffer solution has been determined using X-ray absorption near-edge
spectroscopy (XANES) combined with ab initio calculation. Both active
metal sites have been perfectly reconstructed using suitable initial
str...
The molecular mechanisms for the retrograde motor dynein-dynactin to unload its cargoes at their final destination remain to be elucidated. In this study, we have investigated the regulatory mechanism underlying release of retromer-associated cargoes at the trans-Golgi network (TGN). We report that phosphotidylinositol-4-phosphate (PtdIns(4)P), a G...
Arabidopsis thaliana Deg8, an ATP-independent serine endopeptidase, is involved in the repair of photosystem II (PSII), specifically the degradation of the photo-damaged PSII reaction centre D1 protein. To understand the molecular mechanism underlying the participation of Deg8 in the degradation of the photo-damaged D1 protein, the structure of Deg...
Thioesterase superfamily member 2 (THEM2) is essential for cell proliferation of mammalian cells. It belongs to the hotdog-fold thioesterase superfamily and catalyzes the hydrolysis of the thioester bonds of acyl-CoA in vitro. In this study, THEM2 protein from zebrafish (fTHEM2) was expressed in Escherichia coli and purified by Ni-affinity and gel-...
Fused in sarcoma (FUS) is involved in many processes of RNA metabolism. FUS and another RNA binding protein, TDP-43, are implicated in amyotrophic lateral sclerosis (ALS). It is significant to characterize the RNA recognition motif (RRM) of FUS as its nucleic acid binding properties are unclear. More importantly, abolishing the RNA binding ability...
Arabidopsis thaliana vegetative storage proteins, VSP1 and VSP2, are acid phosphatases and belong to the haloacid dehalogenase (HAD) superfamily. In addition to their potential nutrient storage function, they were thought to be involved in plant defense and flower development. To gain insights into the architecture of the protein and obtain clues a...
Summary of PDB entry validation (PDF).
(PDF)
Summary of hydrophobic contacts between Trn1 and FUS-NLS.
(PDF)
Subcellular localization of WT and mutant FUS in primary mouse dorsal root ganglion (DRG) neurons. GFP-tagged WT full-length human FUS or different ALS mutants (G515C, R522G and P525L) were transfected into DRG neurons. Cells were fixed and permeabilized 48 hours after transfection. The nuclei were stained by 4′,6-diamidino-2-phenylindole (DAPI). T...
Elektronentransferreaktionen des Grün fluoreszierenden Proteins (GFP) aus Quallen können nach Einbau des Metallionen chelatisierenden Tyrosinderivats pyTyr leichter beobachtet werden. In ihrer Zuschrift auf S. 10407 ff. zeigen W. M. Gong, J. Y. Wang et al., dass der lichtinduzierte Elektronentransfer zwischen dem an pyTyr gebundenen CuII‐Ion und de...
SPR analysis of WT and E523Y mutant NLS binding with Trn1. The E523Y mutant bound to Trn1 so tightly that the dissociation of the complex was not observed under the experimental conditions.
(PDF)
Structural properties of the PY fragments of the FUS-NLS (region I) and the other PY-NLS’s. (A) Structural alignment of the PY fragments of the FUS-NLS (yellow; PDB code 4FQ3), hnRNP A1-NLS (blue; PDB code 2H4M), hnRNP D-NLS (grey; PDB code 2Z5N), hnRNP M-NLS (magenta; PDB code 2OT8), and TAP-NLS (cyan; PDB code 2Z5K). (B) N73 and R71 of the TAP-NL...
ET encounters jellyfish: Through the incorporation of the metal-chelating amino acid pyTyr into green fluorescent protein (GFP) from jellyfish, photoinduced electron transfer (ET) from the GFP chromophore to a bound Cu(II) ion was shown to occur within one nanosecond in a distance-dependent manner. The crystal structure of GFP with pyTyr at a speci...
The C-terminal nuclear localization sequence of FUsed in Sarcoma (FUS-NLS) is critical for its nuclear import mediated by transportin (Trn1). Familial amyotrophic lateral sclerosis (ALS) related mutations are clustered in FUS-NLS. We report here the structural, biochemical and cell biological characterization of the FUS-NLS and its clinical implica...
Probing electron‐transfer reactions in green fluorescent protein (GFP) was aided by the incorporation of a metal‐chelating tyrosine derivative, pyTyr. In their Communication on page 10261 ff., W. M. Gong, J. Y. Wang et al. report that photoinduced electron transfer between the pyTyr‐bound CuII ion and the GFP chromophore was distance‐dependent and...
Summary of data-collection and refinement statistics.
(PDF)
Summary of polar/electrostatic interactions between Trn1 and FUS-NLS.
(PDF)
The surface electrostatic potential of Trn1 at the binding site interacting with region I (A), region II (B) and region III (C) of FUS-NLS. The surface interacting with region I and region III are largely neutral whereas the surface interacting with region II is highly negatively charged. FUS-NLS was shown in yellow. (D) The surface properties of t...
Translational GTPases (trGTPases) regulate all phases of protein synthesis. An early event in the interaction of a trGTPase
with the ribosome is the contact of the G-domain with the C-terminal domain (CTD) of ribosomal protein L12 (L12-CTD) and subsequently
interacts with the N-terminal domain of L11 (L11-NTD). However, the structural and functiona...
Eukaryotic organelles have developed elaborate protein quality control systems to ensure their normal activity, among which Deg/HtrA proteases play an essential role. Plant Deg2 protease is a homologue of prokaryotic DegQ/DegP proteases and located in the chloroplast stroma, where its proteolytic activity is required to maintain the efficiency of p...
Coat protein I (COPI) is a protein complex composed of seven subunits that mediates retrograde transport of proteins and lipids from the cis-Golgi network to the endoplasmic reticulum and intra-Golgi membranes. The medium-sized δ subunit of COPI (δ-COP) is a 57 kDa protein with a C-terminal domain (CTD) and an N-terminal longin domain. Here, the δ-...
Arabidopsis thaliana Deg5 is an ATP-independent serine protease which resides on the luminal side of the thylakoid in chloroplasts. Deg5 and another Deg/HtrA-family protease, Deg8, have a synergistic function in the turnover of the D1 protein of photosystem II (PSII), which is prone to damage arising from high light exposure. An inactive mutant of...
Aim:
Human protein disulfide isomerase (hPDI) is a key enzyme and a redox-regulated chaperone responsible for oxidative protein folding in the endoplasmic reticulum. This work aims to reveal the molecular mechanism underlying the redox-regulated functions of hPDI by determining the crystal structures of hPDI in different redox states.
Results:
T...
Not only aliens probe: Iron nitride plays an important role in many catalytic processes, such as Haber–Bosch process, for which knowledge of surface catalytic properties is vital. By using FTIR spectroscopic techniques, this work describes the surface active sites of iron nitride/fumed SiO2 by coupled with CO, NH3, and H2 as probe- molecules. Inter...
Human ankyrin repeat and suppressor of cytokine signaling box protein 9 (hASB9) is a specific substrate-recognition subunit of an elongin C-cullin-SOCS box E3 ubiquitin ligase complex. It recognizes its substrate, brain type creatine kinase (CKB), using the ankyrin repeat domain; and facilitates the polyubiquitination of CKB to mediate proteasomal...
When elongation factor G (EF-G) binds to the ribosome, it first makes contact with the C-terminal domain (CTD) of L12 before interacting with the N-terminal domain (NTD) of L11. Here we have identified a universally conserved residue, Pro22 of L11, that functions as a proline switch (PS22), as well as the corresponding center of peptidyl-prolyl cis...
As a large family of hydrolases, GTPases are widespread in cells and play the very important biological function of hydrolyzing GTP into GDP and inorganic phosphate through binding with it. GTPases are involved in cell cycle regulation, protein synthesis, and protein transportation. Chaperones can facilitate the folding or refolding of nascent pept...
Symmetric and asymmetric dimethylation of arginine are isomeric protein posttranslational modifications with distinct biological effects, evidenced by the methylation of arginine 3 of histone H4 (H4R3): symmetric dimethylation of H4R3 leads to repression of gene expression, while asymmetric dimethylation of H4R3 is associated with gene activation....
Defensins are key players of the innate immune system known to act against bacteria, fungi and viruses. Here we report the 0.98-Å crystal structure of SPE10, a dimeric plant defensin. SPE10 associates as a dimer through a unique amino acid triplet involving residues R36-W42-R40. The helix from one subunit interacts with arginines R36 and R40 from t...
Research has shown that the palmitoyl group of α-tubulin mediates the hydrophobic interaction between microtubules and intracellular membranes and that palmitoylated tubulin plays a role in signal transduction. There are 20 cysteine residues per α/β tubulin heterodimer. C376 of α-tubulin was reported to be predominantly palmitoylated and C20, C213...
Maintenance of the Golgi apparatus (GA) structure and function depends on Golgi matrix proteins. The posttranslational modification of Golgi proteins such as phosphorylation of members of the golgin and GRASP families is important for determining Golgi architecture. Some Golgi proteins including golgin-84 are also known to be methylated, but the fu...
Piwi proteins are modified by symmetric dimethylation of arginine (sDMA), and the methylarginine-dependent interaction with Tudor domain proteins is critical for their functions in germline development. Cocrystal structures of an extended Tudor domain (eTud) of Drosophila Tudor with methylated peptides of Aubergine, a Piwi family protein, reveal th...
We used X-ray absorption near edge structure (XANES) spectroscopy to investigate the metal-dependent enzymatic activity of the peptide deformylase from Leptospira interrogans (LiPDF). Ab initio full multiple scattering calculations performed by MXAN are applied to obtain the local structure of the cobalt-containing LiPDF (Co-LiPDF) and zinc-contain...
Eukaryotic translation initiation factor eIF2B, the guanine nucleotide exchange factor (GEF) for eIF2, catalyzes conversion of eIF2·GDP to eIF2·GTP. The eIF2B is composed of five subunits, α, β, γ, δ and ɛ, within which the ɛ subunit is responsible for catalyzing the guanine exchange reaction. Here we present the crystal structure of the C-terminal...
The cyclic AMP receptor protein (CRP) from Escherichia coli regulates the expression of a large number of genes. In this work, CRP has been overexpressed, purified and digested by subtilisin and chymotrypsin. The fragments S-CRP (digested by subtilisin) and CH-CRP (digested by chymotrypsin) have been purified and crystallized. Crystals of S-CRP dif...
Histone deacetylase 6 (HDAC6) is a cytosolic enzyme that catalyzes deacetylation of several proteins. Acetylated tubulin has been recently identified as a physiological substrate of HDAC6. However in previous reports, all in vitro binding and enzymatic assays were accomplished with only partially purified protein samples. Therefore, it still remain...
Adenylate kinase 4 (AK4) is a unique member with no enzymatic activity in vitro in the adenylate kinase (AK) family although it shares high sequence homology with other AKs. It remains unclear what physiological function AK4 might play or why it is enzymatically inactive. In this study, we showed increased AK4 protein levels in cultured cells expos...
Synbindin is one component of Transport protein particle (TRAPP) complexes. In the hippocampal neurons, synbindin binds syndecan-2 by its atypical PDZ domain (APD) and may regulate the formation of dendritic spines. To investigate the interaction of synbindin and syndecan-2, we determined the solution structure of the synbindin APD by NMR. The stru...
The focus of this paper is the hotdog-fold thioesterase THEM2 from human (hTHEM2; Swiss-Prot entry Q9NPJ3 ). In an earlier communication (Cheng, Z., Song, F., Shan, X., Wei, Z., Wang, Y., Dunaway-Mariano, D., and Gong, W. (2006) Crystal structure of human thioesterase superfamily member 2, Biochem. Biophys. Res. Commun. 349, 172-177) we reported th...
It is well known that motion of LID and NMP-binding (NMP(bind)) domains in adenylate kinase (AK) is important in ligand binding and catalysis. However, the nature of such domain motions is poorly characterized. One of the critical hinge regions is hinge IV, which connects the CORE and LID domains. In addition, the hinge IV contains a strictly conse...
Previous results suggest that methylotrophic yeasts may contain factors that modulate prion stability. Alcohol oxidase (AOX), a key enzyme in methanol metabolism, is an abundant protein that is specific to methylotrophic yeasts. We examined the effect of Pichia pastoris AOX1 on prion phenotypes in Saccharomyces cerevisiae. The S. cerevisiae prion s...
Ni-dependent carbon monoxide dehydrogenases (Ni-CODHs) are a diverse family of enzymes that catalyze reversible CO:CO2 oxidoreductase activity in acetogens, methanogens, and some CO-using bacteria. Crystallography of Ni-CODHs from CO-using bacteria and acetogens has revealed the overall fold of the Ni-CODH core and has suggested structures for the...
Transport protein particle (TRAPP) is a large multiprotein complex that involves in ER-to-Golgi and intra-Golgi traffic. Synbindin, the human ortholog of yeast Trs23, is one component of the TRAPP complexes. In the hippocampal neurons the synbindin/syndecan complex is involved in synaptic membrane trafficking and thereby regulates the formation of...
Homoserine O-acetyltransferase (HTA, EC 2.3.1.31) initiates methionine biosynthesis pathway by catalyzing the transfer of acetyl group from acetyl-CoA to homoserine. This study reports the crystal structure of HTA from Leptospira interrogans determined at 2.2A resolution using selenomethionyl single-wavelength anomalous diffraction method. HTA is m...
Citations
... However, GPR84 has a significantly broader expression pattern, including in brown adipocytes where it seems to play an important role in mitochondrial function (Sun et al., 2023). Moreover, in addition to the potential use of antagonists of GPR84 in the treatment of inflammatory conditions, such as ulcerative colitis and in liver, lung and kidney fibrosis, activators of GPR84 have been suggested to be useful agents to promote cancer cell phagocytosis (Kamber et al., 2021;Zhang et al., 2023). Since the symposium was held, perhaps the most important advances in understanding the pharmacology of GPR84 have been the publication of atomic level cryo-Electron Microscopy structures of GPR84 bound by the synthetic agonists 6-n-octylaminouracil (6-OAU; Zhang et al., 2023) and 6-nonylpyridine-2,4-diol (LY-237; Liu et al., 2023) or the MCFA 3-hydroxylauric acid . ...
Reference: Editorial for GPR84 pharmacology
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... Because tP4H does not have an experimental structure, we identified these active site residues using an Alphafold2 35 model ( Figure S6) and comparisons to structures of the highly homologous Fe(II)/αKG enzyme GriE. 36,37 In all cases active site mutations produced activity decreases for the non-native substrate 1 ( Figure 2). We also observed increased product yield with increasing wild-type tP4H concentration ( Figure 2). ...
... Another example of a pro-phagocytic receptor is the G protein-coupled receptor (GPCR), specifically GPR84. GPR84 is found to be upregulated in AML leukemic stem cells and expression of this GPR member is correlated with significantly overall survival of patients diagnosed with acute myeloid leukemia (AML) (14,15). In this context it is worthwhile to note that several of the other much less researched SIRP family members may also be of therapeutic interest. ...
... To further confirm the importance of G3BP1 in promoting the ubiquitination activity of TRIM25, we assessed two different G3BP1 mutants (TBM: TRIM25-binding mutant and GDM: G3BP1-dimer mutant) in the in vitro ubiquitination assay. We and others have previously identified three bulky hydrophobic amino acids (F15, F33, F124) in the NTF2 domain of G3BP1 that were critical for binding to the ΦxFG motif-containing peptide 25,60 , and the TBM mutant (F15A, F33A, F124A) disrupted the TRIM25-G3BP1 interaction. Similarly, structural analysis revealed three amino acids (D81, H83, Q93) responsible for the homodimerization of G3BP1 (Fig. S6f), and the GDM mutant (D81K, H83A, Q93A) were expected to weaken the dimerization. ...
... ABC transporters are involved in a variety of important transportation processes in organisms, which necessitate the participation of functional activity from both nucleotidebinding domains (NBDs) and transmembrane domains (TMDs) [44,45]. The TMDs contribute to mycobacterial pathogenesis by secreting virulence factors and promoting antibiotic efflux [46]. For instance, the deletion of MSMEG3763 enhances the susceptibility of Ms relative to antimicrobial drugs, which are classified as transmembrane polypeptides belonging to the ABC efflux pump in the MSMEG3762-MSMEG3763-MSMEG3765 operon of Ms [47]. ...
... Subsequently, detergent was removed and proteoliposome formation was performed by dialysis for 1 week at 100× dilution against 1 liter of 20 mM tris-HCl and 150 mM NaF (pH 7.5) to obtain "high-F − sample", while dialysis for 1 week or at least 3 months at 100× dilution against 1 liter of 20 mM tris-HCl and 150 mM NaCl (pH 7.5) to obtain a low-F − sample and an F − -free sample, respectively. The reconstituted proteoliposomes were collected by ultracentrifugation at 180,000g for 4 hours at 4°C. 19 F-labeled protein was expressed and purified by incorporating the unnatural amino acid tfmF into the specific site as previously described (41). The Fluc-Ec1 F89tfmF mutant was performed by site-directed mutagenesis. ...
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... Common enzymes applied for CO 2 reduction include CO dehydrogenase and formate dehydrogenase [84][85][86] , whose preparations require laborious purification 97,98 . Elaborately designed enzymes can be fabricated through genetic engineering and overexpression 87,88 . To eliminate the extensive purification process of isolating enzymes, bacteria cocatalysts such as Moorella thermoacetica 92,99 and Sporomusa ovata 91 have been directly used. ...
Reference: Photocatalytic CO2 reduction
... 5 Structural studies have provided insights into the molecular mechanism of gene editing by Cas12i1 and Cas12i2, offering important information for optimizing Cas12i family nucleases. [6][7][8] Recently, Zhang et al. identified a new Cas12i nuclease and generated a robust version, hfCas12Max, via protein engineering. 9 Nevertheless, several Cas12i nucleases remain poorly characterized, providing opportunities for further development. ...
... Some enzymes , such as βglucosidase (BGL), increase antioxidant capacity by releasing phenolic compounds (Serventi et al. 2020 ). Some yeast strains of the Pichia and Hansenula genera are good producer of BGL that impr ov e wine flavor and aroma (Yang et al. 2020, Vicente et al. 2021. Huang et al. ( 2021 ) reported that species such as Clavispora lusitaniae , Hanseniaspora guilliermondii , M. pulcherrima and W. anomalus show high BGL activity under aerobic conditions. ...
... This approach involves the use of orthogonal transfer RNAs (tRNAs) and aminoacyl-tRNA synthetases (aaRSs) to replace the chromophore-forming tyrosine of GFP with a designed ncAA [30][31][32][33]. Through this method, several ncAA-derived variants of GFP with red-shifted fluorescence have been successfully developed [34,35]. In previous studies, our research group and others have demonstrated the use of 3-aminotyrosine (aY), a specific ncAA, to modify the GFP chromophore [36,37], leading to consistent red-shifting of the spectra in GFPs, circularly permuted GFPs (cpGFPs), and GFP-based biosensors. ...
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