Biomedical subjects

Zhiyi Wei

Publications and source records attributed to Zhiyi Wei.

At least 19 recordsLinked to original sources

PubMed2006

Crystal structures of E. coli laccase CueO at different copper concentrations.

CueO protein is a hypothetical bacterial laccase and a good laccase candidate for large scale industrial application. Four CueO crystal structures were determined at different copper concentrations. Low copper occupancy in apo-CueO and slow copper reconstitution process in CueO with exogenous copper were demonstrated. These observations well explain the copper dependence of CueO oxidase activity. Structural comparison between CueO and other three fungal laccase proteins indicates that Glu106 in CueO constitutes the primary counter-work for reconstitution of the trinuclear copper site. Mutation of Glu106 to a Phe enhanced CueO oxidation activity and supported this hypothesis. In addition, an extra alpha-helix from Leu351 to Gly378 covers substrate biding pocket of CueO and might compromises the electron transfer from substrate to type I copper.

Amino Acid Sequence↗

PubMed2006

Crystal structures of human IPP isomerase: new insights into the catalytic mechanism.

Type I isopentenyl diphosphate (IPP): dimethylally diphosphate (DMAPP) isomerase is an essential enzyme in human isoprenoid biosynthetic pathway. It catalyzes isomerization of the carbon-carbon double bonds in IPP and DMAPP, which are the basic building blocks for the subsequent biosynthesis. We have determined two crystal structures of human IPP isomerase I (hIPPI) under different crystallization conditions. High similarity between structures of human and Escherichia coli IPP isomerases proves the conserved catalytic mechanism. Unexpectedly, one of the hIPPI structures contains a natural substrate analog ethanol amine pyrophosphate (EAPP). Based on this structure, a water molecule is proposed to be the direct proton donor for IPP and different conformations of IPP and DMAPP bound in the enzyme are also proposed. In addition, structures of human IPPI show a flexible N-terminal alpha-helix covering the active pocket and blocking the entrance, which is absent in E. coli IPPI. Besides, the active site conformation is not the same in the two hIPPI structures. Such difference leads to a hypothesis that substrate binding induces conformational change in the active site. The inhibition mechanism of high Mn(2+) concentrations is also discussed.

Amino Acid Sequence↗

PubMed2006

Seeing the process of histidine phosphorylation in human bisphosphoglycerate mutase.

Bisphosphoglycerate mutase is an erythrocyte-specific enzyme catalyzing a series of intermolecular phosphoryl group transfer reactions. Its main function is to synthesize 2,3-bisphosphoglycerate, the allosteric effector of hemoglobin. In this paper, we directly observed real-time motion of the enzyme active site and the substrate during phosphoryl transfer. A series of high resolution crystal structures of human bisphosphoglycerate mutase co-crystallized with 2,3-bisphosphoglycerate, representing different time points in the phosphoryl transfer reaction, were solved. These structures not only clarify the argument concerning the substrate binding mode for this enzyme family but also depict the entire process of the key histidine phosphorylation as a "slow movie". It was observed that the enzyme conformation continuously changed during the different states of the reaction. These results provide direct evidence for an "in line" phosphoryl transfer mechanism, and the roles of some key residues in the phosphoryl transfer process are identified.

2,3-Diphosphoglycerate↗

PubMed2006

Crystal structure of human thioesterase superfamily member 2.

Hotdog-fold has been identified in more than 1000 proteins, yet many of which in eukaryotes are less studied. No structural or functional studies of human thioesterase superfamily member 2 (hTHEM2) have been reported before. Since hTHEM2 exhibits about 20% sequence identity to Escherichia coli PaaI protein, it was proposed to be a thioesterase with a hotdog-fold. Here, we report the crystallographic structure of recombinant hTHEM2, determined by the single-wavelength anomalous dispersion method at 2.3A resolution. This structure demonstrates that hTHEM2 indeed contains a hotdog-fold and forms a back-to-back tetramer as other hotdog proteins. Based on structural and sequence conservation, the thioesterase active site in hTHEM2 is predicted. The structure and substrate specificity are most similar to those of the bacterial phenylacetyl-CoA hydrolase. Asp65, located on the central alpha-helix of subunit B, was shown by site-directed mutagenesis to be essential to catalysis.

Amino Acid Sequence↗

PubMed2006

Diode-pumped continuous-wave Nd:LuVO4 laser operating at 916 nm.

We realized an efficient diode-pumped Nd:LuVO4 continuous-wave (CW) laser operating at 916 nm. Laser experiments with 0.5 at. % Nd-doped Nd:LuVO4 crystals of various lengths and cutting directions were also investigated. The maximum output power of 930 mW was obtained with a slope efficiency of 27.2% and an optical conversion efficiency of 20.8% at the absorbed pump power of 4.5 W. The laser experiment shows that Nd:LuVO4 crystal can be used for an efficient diode-pumped laser system.

Journal Article↗

PubMed2006

Low-threshold self-starting femtosecond Ti:sapphire laser.

A low-threshold self-starting Kerr-lens mode-locked Ti:sapphire laser is demonstrated that uses a tight-focusing cavity design in conjunction with a semiconductor saturable-absorber mirror (SESAM). With 3% and 12% output couplers, we achieve mode-locking thresholds as low as 390 and 600 mW, respectively. Stable femtosecond laser pulses with average power of 114 mW are generated at a pump power of 1.2 W, which corresponds to a typical duration of 17 fs and bandwidth of 47 nm. Mode-locking operation is achieved in a pump power range of 600 mW to 4.8 W at an output coupling of 12%; the advantages of using a SESAM for low-power mode-locking operation are demonstrated.

Journal Article↗

PubMed2006

Crystal structure of the C-terminal domain of S.cerevisiae eIF5.

eIF5, a GTPase-activating protein (GAP) specific for eIF2, plays a critical role in pre-initiation complex assembly and correct AUG selection during eukaryotic translation initiation. eIF5 is involved in the formation of the multifactor complex (MFC), an important intermediate of the 43S pre-initiation complex. The C-terminal domain (CTD) of eIF5 functions as the structural core in the MFC assembly. Here we report the 1.5A crystal structure of eIF5-CTD, confirming that eIF5-CTD contains an atypical HEAT motif. In addition, analyzing the electrostatic potential and the distribution of conserved residues on the protein surface, we confirm and suggest some potential regions of interactions between eIF5-CTD and other eIFs. The structure of eIF5-CTD provides useful information in understanding the mechanism of the MFC assembly.

Amino Acid Sequence↗

PubMed2006

Crystal structure of a papain-fold protein without the catalytic residue: a novel member in the cysteine proteinase family.

A 31kDa cysteine protease, SPE31, was isolated from the seeds of a legume plant, Pachyrizhus erosus. The protein was purified, crystallized and the 3D structure solved using molecular replacement. The cDNA was obtained by RT PCR followed by amplification using mRNA isolated from the seeds of the legume plant as a template. Analysis of the cDNA sequence and the 3D structure indicated the protein to belong to the papain family. Detailed analysis of the structure revealed an unusual replacement of the conserved catalytic Cys with Gly. Replacement of another conserved residue Ala/Gly by a Phe sterically blocks the access of the substrate to the active site. A polyethyleneglycol molecule and a natural peptide fragment were bound to the surface of the active site. Asn159 was found to be glycosylated. The SPE31 cDNA sequence shares several features with P34, a protein found in soybeans, that is implicated in plant defense mechanisms as an elicitor receptor binding to syringolide. P34 has also been shown to interact with vegetative storage proteins and NADH-dependent hydroxypyruvate reductase. These roles suggest that SPE31 and P34 form a unique subfamily within the papain family. The crystal structure of SPE31 complexed with a natural peptide ligand reveals a unique active site architecture. In addition, the clear evidence of glycosylated Asn159 provides useful information towards understanding the functional mechanism of SPE31/P34.

Amino Acid Sequence↗

PubMed2005

The crystal structure of putative precorrin isomerase CbiC in cobalamin biosynthesis.

The leptospira cbiC encodes the enzyme catalyzing the methyl rearrangement reaction of the cobalamin biosynthesis pathway. The protein has been cloned and overexpressed as a His-tagged recombinant protein in Escherichia coli. The crystal structures have been solved in two crystal forms (P4(2)2(1)2 and P3(1)21) diffracting to 3.0 and 2.3A resolution, respectively. The structures are similar to the precorrin-8x methyl mutase (CobH), an enzyme of the aerobic pathway to vitamin B12.

Amino Acid Sequence↗

PubMed2005

Crystal structure of human guanosine monophosphate reductase 2 (GMPR2) in complex with GMP.

Guanosine monophosphate reductase (GMPR) catalyzes the irreversible and NADPH-dependent reductive deamination of GMP to IMP, and plays a critical role in re-utilization of free intracellular bases and purine nucleosides. Here, we report the first crystal structure of human GMP reductase 2 (hGMPR2) in complex with GMP at 3.0 A resolution. The protein forms a tetramer composed of subunits adopting the ubiquitous (alpha/beta)8 barrel fold. Interestingly, the substrate GMP is bound to hGMPR2 through interactions with Met269, Ser270, Arg286, Ser288, and Gly290; this makes the conformation of the adjacent flexible binding region (residues 268-289) fixed, much like a door on a hinge. Structure comparison and sequence alignment analyses show that the conformation of the active site loop (residues 179-187) is similar to those of hGMPR1 and inosine monophosphate dehydrogenases (IMPDHs). We propose that Cys186 is the potential active site, and that the conformation of the loop (residues 129-133) suggests a preference for the coenzyme NADPH over NADH. This structure provides important information towards understanding the functions of members of the GMPR family.

Amino Acid Sequence↗

PubMed2005

Independently tunable 1.3 W femtosecond Ti:sapphire lasers passively synchronized with attosecond timing jitter and ultrahigh robustness.

A stable passively synchronized femtosecond laser has been realized by coupling two 1.3 W mode-locked Ti:sapphire lasers with a Kerr medium. An ultralong tolerance of 10 microm for the cavity length mismatch and a timing jitter of less than 0.4 fs were obtained. The relative carrier-envelope phase slip was directly observed by measuring the heterodyne output between the two lasers.

Journal Article↗

PubMed2005

Crystal structure of human B-type phosphoglycerate mutase bound with citrate.

The B-type cofactor-dependent phosphoglycerate mutase (dPGM-B) catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate in glycolysis and gluconeogenesis pathways using 2,3-bisphosphoglycerate as the cofactor. The crystal structures of human dPGM-B bound with citrate were determined in two crystal forms. These structures reveal a dimerization mode conserved in both of dPGM and BPGM (bisphosphoglycerate mutase), based on which a dPGM/BPGM heterodimer structure is proposed. Structural comparison supports that the conformational changes of residues 13-21 and 98-117 determine PGM/BPGM activity differences. The citrate-binding mode suggests a substrate-binding model, consistent with the structure of Escherichia coli dPGM/vanadate complex. A chloride ion was found in the center of the dimer, providing explanation for the contribution of chloride ion to dPGM activities. Based on the structural information, the possible reasons for the deficient human dPGM mutations found in some patients are also discussed.

Amino Acid Sequence↗

PubMed2005

Polarization-dependent supercontinuum generation from light filaments in air.

We investigate polarization-dependent properties of the supercontinuum emission generated from filaments produced by intense femtosecond laser pulses propagating through air over a long distance. The conversion efficiency from the 800-nm fundamental to white light is observed to be higher for circular polarization than for linear polarization when the laser intensity exceeds the threshold of the breakdown of air.

Journal Article↗

PubMed2004

Crystal structure of human coactosin-like protein.

Human coactosin-like protein is an actin filament binding protein but does not bind to globular actin. It associates with 5-Lipoxygenase both in vivo and in vitro, playing important roles in modulating the activities of actin and 5-Lipoxygenase. Coactosin counteracts the capping activity of capping protein which inhibits the actin polymerization. We determined the crystal structures of human coactosin-like protein by multi-wavelength anomalous dispersion method. The structure showed a high level of similarity to ADF-H domain, although their amino acid sequences share low degree of homology. A few conserved hydrophobic residues that may contribute to the folding were identified. This structure suggests coactosin-like protein bind to F-actin in a different way from ADF/Cofilin family. Combined with the information from previous mutagenesis studies, the binding sites for F-actin and 5-Lipoxygenase were analyzed, respectively. These two sites are quite close, which might prevent F-actin and 5-Lipoxygenase from binding to coactosin simultaneously.

Actin Depolymerizing Factors↗

PubMed2004

Cloning, purification, crystallization and preliminary crystallographic analysis of human phosphoglycerate mutase.

Human B-type 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (dPGM-B) has been cloned, overexpressed and purified, with a yield of 30% of the total protein. Crystals of human dPGM-B were obtained using the hanging-drop vapour-diffusion technique. X-ray diffraction data were collected to 2.8 A resolution. The human dPGM-B crystals belong to space group P2(1), with unit-cell parameters a = 130.5, b = 75.9, c = 187.0 A, beta = 94.4 degrees. There could be between 9 and 18 monomers per asymmetric unit, with 12 molecules being the most likely.

Brain↗

PubMed2004

Crystal structure of human bisphosphoglycerate mutase.

Bisphosphoglycerate mutase is a trifunctional enzyme of which the main function is to synthesize 2,3-bisphosphoglycerate, the allosteric effector of hemoglobin. The gene coding for bisphosphoglycerate mutase from the human cDNA library was cloned and expressed in Escherichia coli. The protein crystals were obtained and diffract to 2.5 A and produced the first crystal structure of bisphosphoglycerate mutase. The model was refined to a crystallographic R-factor of 0.200 and R(free) of 0.266 with excellent stereochemistry. The enzyme remains a dimer in the crystal. The overall structure of the enzyme resembles that of the cofactor-dependent phosphoglycerate mutase except the regions of 13-21, 98-117, 127-151, and the C-terminal tail. The conformational changes in the backbone and the side chains of some residues reveal the structural basis for the different activities between phosphoglycerate mutase and bisphosphoglycerate mutase. The bisphosphoglycerate mutase-specific residue Gly-14 may cause the most important conformational changes, which makes the side chain of Glu-13 orient toward the active site. The positions of Glu-13 and Phe-22 prevent 2,3-bisphosphoglycerate from binding in the way proposed previously. In addition, the side chain of Glu-13 would affect the Glu-89 protonation ability responsible for the low mutase activity. Other structural variations, which could be connected with functional differences, are also discussed.

Amino Acid Sequence↗

PubMed2004

Crystal structure of human eIF3k, the first structure of eIF3 subunits.

eIF3k, the smallest subunit of eukaryotic initiation factor 3 (eIF3), interacts with several other subunits of eIF3 and the 40 S ribosomal subunit. eIF3k is conserved among high eukaryotes, including mammals, insects, and plants, and it is ubiquitously expressed in human tissues. Interestingly, eIF3k does not exist in some species of yeast. Thus, eIF3k may play a unique regulatory role in higher organisms. Here we report the crystal structure of human eIF3k, the first high-resolution structure of an eIF3 component. This novel structure contains two distinct domains, a HEAT (named for Huntington, elongation factor 3, A subunit of protein phosphatase 2A, target of rapamycin) repeat-like HAM (HEAT analogous motif) domain and a winged-helix-like WH domain. Through structural comparison and sequence conservation analysis, we show that eIF3k has three putative protein-binding surfaces and has potential RNA binding activity. The structure provides key information for understanding the structure and function of the eIF3 complex.

Amino Acid Motifs↗

PubMed2003

Control of relative carrier-envelope phase slip in femtosecond Ti:sapphire and Cr:forsterite lasers.

We were able to control relative carrier-envelope phase slip among mode-locked Ti:sapphire and Cr:forsterite lasers by employing electronic feedback. The pulse timings of these lasers were passively synchronized with our crossing-beam technique. Since the optical-frequency ratio of Ti:sapphire and Cr:forsterite is approximately 3:2, we can observe the phase relation by superimposing the third harmonic of Cr:forsterite and the second harmonic of Ti:sapphire lasers in time and in space. The spectrum width of the locked beat note was less than 3 kHz, which corresponds to the controlled fluctuation of a cavity-length difference of less than 10 pm.

Journal Article↗