The important and diverse regulatory roles of Ca(2+) in eukaryotes are conveyed by the EF-hand containing calmodulin superfamily. However, the calcium-regulatory proteins in prokaryotes are still poorly understood. In this study, we report the three-dimensional structure of the calcium-binding protein from Streptomyces coelicolor, named CabD, which shares low sequence homology with other known helix-loop-helix EF-hand proteins. The CabD structure should provide insights into the biological role of the prokaryotic calcium-binding proteins. The unusual structural features of CabD compared with prokaryotic EF-hand proteins and eukaryotic sarcoplasmic calcium-binding proteins, including the bending conformation of the first C-terminal α-helix, unpaired ligand-binding EF-hands and the lack of the extreme C-terminal loop region, suggest it may have a distinct and significant function in calcium-mediated bacterial physiological processes, and provide a structural basis for potential calcium-mediated regulatory roles in prokaryotes.
Amino Acid Sequence ; Binding Sites ; Calcium ; physiology ; Calcium-Binding Proteins ; chemistry ; Crystallography, X-Ray ; EF Hand Motifs ; Molecular Sequence Data ; Protein Binding ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Homology, Amino Acid ; Streptomyces coelicolor ; Structural Homology, Protein ; Surface Properties

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 domain of human eIF2Bɛ (eIF2Bɛ-CTD) at 2.0-Å resolution. The structure resembles a HEAT motif and three charge-rich areas on its surface can be identified. When compared to yeast eIF2Bɛ-CTD, one area involves highly conserved AA boxes while the other two are only partially conserved. In addition, the previously reported mutations in human eIF2Bɛ-CTD, which are related to the loss of the GEF activity and human VWM disease, have been discussed. Based on the structure, most of such mutations tend to destabilize the HEAT motif.
Amino Acid Motifs ; Amino Acid Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Eukaryotic Initiation Factor-2B ; biosynthesis ; chemistry ; Humans ; Molecular Sequence Data ; Protein Structure, Tertiary ; Protein Subunits ; biosynthesis ; chemistry ; Recombinant Proteins ; biosynthesis ; chemistry ; Sequence Alignment ; Structural Homology, Protein ; Surface Properties

The nucleotide sequence and N-, C-terminal amino acid sequences of alpha,beta-subunit of glutaryl 7-ACA acylase C130 from Pseudomonas sp. 130 were determined. The alignment of the acylase C130 with the other acylases shows that it has high homology with the acylases from Pseudomonas sp. GK16 and C427, but low homology with the others. There is large difference in the N-terminal of alpha-subunit, while the N-terminal of beta-subunit has significant conservation.
Amino Acid Sequence ; Base Sequence ; DNA, Bacterial ; analysis ; Genes, Bacterial ; Molecular Sequence Data ; Penicillin Amidase ; genetics ; Pseudomonas ; enzymology ; genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid

OBJECTIVETo study the EV71 Chinese strain SHZH98 and analyze its genetic evolution using 3c gene as index.

METHODSThe 3C gene cDNA of EV71 Chinese strain SHZH98 was amplified by PCR, the PCR product was sequenced.

RESULTSThe EV71 Chinese mainland strain SHZH98 3C segment was 549 bps in length. Comparison of nucleotide sequences from other enteroviruses which have been published, revealed a higher homology to strain MS, 78.7% at nucleotide level and 93.45% at deduced amino acid level. The homology to strain BrCr was 76.7% at nucleotide level and 89.1% at deduced amino acid level. Taiwan strains POLY,NCKU,TW2086,TW2272 shared a lower homology with Chinese mainland strain SHZH98, 74.0%, 73.8%, 71.9%, 69.8% at nucleotide level and 90.7%, 90.2%, 84.2%, 82.5% at deduced amino acid level. The genetic progress analysis revealed that EV71 Chinese mainland strain SHZH98 3C segment shares more homology with European and American strains than Taiwan strains.

CONCLUSIONThe non-structural protein of EV71 Chinese strains may have different evolutionary process from Taiwan strains.

Amino Acid Sequence ; Base Sequence ; Enterovirus ; genetics ; isolation & purification ; Genes, Viral ; Humans ; Molecular Sequence Data ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid

OBJECTIVETo investigate the genetic characteristics of coxsackievirus A10(CV-A10) strains isolated from hand, foot and mouth disease (HFMD) cases in Ningxia province.

METHODSBased on the HFMD laboratory network surveillance system, 2 470 patients clinical specimens including 450 faeces and 2 020 throat swaps were collected from various regions people's hospital in Ningxia Hui Autonomous Region during January, 2013 to December, 2014. All specimens were isolated using rhabdomyosarcoma cells. VP1 regional gene of isolated strains was amplified by RT-PCR using degenerate primers and sequenced. Sequences were compared with the database of GenBank by the Blast algorithm to identify the enterovirus genotypes. All the CV-A10 strains were performed the homology and phylogenetic evolution analysis.

RESULTS450 specimens identified as non-EV-A71, non-CV-A16 enterovirus were collected and 36 CV-A10 strains were isolated, 6 strains were isolated in 2013 and 30 strains were isolated in 2014. The homology of nucleotides and amino acids among 36 CV-A10 strains were 90.6%-100.0% , and 90.2%-100.0%, respectively. Compared 36 strains with genotype A, B, C, D representative strains, it has the highest homology with the genotype C, the nucleotide and amino acids homogeneity were 90.2%-98.9% and 95.7%-99.7%. The phylogenetic tree showed 36 strains and genotype C representative strains located in the same evolutionary branch.

CONCLUSIONCV-A10 was one of the most common pathogen of HFMD in Ningxia Hui Autonomous Region. All CV-A10 strains belonged to genotype C and contained wide homology range.

China ; Enterovirus ; genetics ; Genotype ; Hand, Foot and Mouth Disease ; virology ; Humans ; Phylogeny ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid

Human defensin is a family of cationic antimicrobial peptides in human being. During the last two decades a series of endogenous alpha-and beta-human defensins have been discovered. They are important components of the first barrier in human's body against the invasion of various microorganisms, and they are thought to play an important role in linking the innate and adaptive defense system of human being. The recent advances in the research of human defensins were reviewed, including their discovery, molecular and genetic properties, expression regulation, and mechanisms of antimicrobial activity. The possibility to produce human defensins via genetic engineering was also discussed. And the application outlook of human defensins in medicine and curing patients infected with antibiotics-resistant microbials was presented.
Amino Acid Sequence ; Defensins ; chemistry ; genetics ; metabolism ; physiology ; Genetic Engineering ; Humans ; Molecular Sequence Data ; Sequence Homology, Amino Acid

This paper is to show a way of acqusition of the variable region gene of rabbit osteoprotegerin (OPG) and to analyse series. Total RNA was extracted from rabbit tibia, transcripted reversely into cDNA with random primers. The variable region of the OPG gene ampliflied using 5'RACE. Sequencing was confirmed by agarose gel electrophoresis and sequencing analysis. Full length of OPG gene was 1540bp that encoding 400 amino acids. It shared 89% identity with human OPG in whole amino acid sequence and about 85% with rattus norvegicus and other mammal. The OPG sequence of rabbit was obtained by 5'RACE, which could provide a good basis for OPG functional study.
Animals ; Base Sequence ; Molecular Sequence Data ; Osteoprotegerin ; genetics ; Rabbits ; Sequence Homology, Amino Acid

The nonstructural protein 4 (NSP4) of rotavirus encoded by gene 10, plays an important role in rotavirus pathogenicity. In this study, NSP4 gene sequences of human rotaviruses circulating in Seoul, Korea between March 2004 and April 2005 were determined. The nucleotide sequence data indicated that the NSP4 genes of human rotavirus Korean isolates were 750 or 751 bases in length and encoded one open reading frame of 175 amino acids with two glycosylation sites. The NSP4 of Korean isolates exhibited amino acid sequence homologies between 59.4% and 98.9%. The NSP4 of CAU4 and CAU15 showed a high degree of amino acid sequence homologies with NSP4 genotype A viruses, but the NSP4 of CAU5, CAU6, CAU11, CAU14, CAU16 and CAU22 exhibited a high degree of amino acid sequence homologies with NSP4 genotype B viruses. Interestingly, CAU3 and CAU7 showed low degree of amino acid sequence homology with those of currently described NSP4 genotypes A to D and belonged a distinct lineage on the phylogenetic tree. These findings suggests that distinct NSP4 type was circulating among human rotavirus strains in the local community of Seoul and raising intriguing questions regarding possible explanations for new genotype.
Amino Acid Sequence ; Amino Acids ; Base Sequence ; Genetic Variation* ; Genotype ; Glycosylation ; Herpesvirus 1, Cercopithecine ; Humans* ; Korea ; Open Reading Frames ; Rotavirus* ; Seoul* ; Sequence Homology, Amino Acid ; Virulence

OBJECTIVETo characterize HA1 gene of influenza B virus circulated in 1990 through 2000 in China.

METHODSViral RNA was extracted and transcribed into cDNA by reverse transcriptase and amplified by PCR. The product of PCR was purified and sequenced by ABI377. The sequence data were analyzed with epidemic records.

RESULTS1. Two major lineages of influenza B virus always circulated during the period of 1990-2000 in China; the Yamagata lineage was the main lineage, but in 1994 and 1997 the Victoria lineage was more active. 2. During 1992-2000 the Yamagata lineage evolved into two minor groups whose distance in HAI amino acid sequences was about 6%. 3. Large and non-reverse mutators led the development of influenza B epidemics in 1990-2000 in China. 4. Except for a few strains, there was little difference among the influenza B viruses of the same major lineages circulated in the same year in China.

CONCLUSIONSTwo major lineages of influenza B virus always circulated during the period from 1990-2000 in China,and the Yamagata lineage diverged into two minor groups in recent years. Exchanges of the lineages and the appearance of large non-reverse mutators possibly had important epidemic significance.

China ; epidemiology ; Genes, Viral ; genetics ; Influenza B virus ; classification ; genetics ; RNA, Viral ; genetics ; Sequence Analysis ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid

A full-length cDNA of GGPPS gene from Tripterygium wilfordii suspension cells was obtained by use of RACE strategy (GeneBank: KM978333), and then analyzed by bioinformatics approaches. TwGGPPS cDNA has 1857 nucleotides and an open reading frame (ORF) encoding a protein of 514 amino acid residues. The deduced protein has isoelectric point (pI) of 7.85, a calculated molecular weight about 57.13 kD, 5 conserved domains and 2 functional domains. PSORT Prediction showed it was located at plasma membrane. Phylogenetic analysis demonstrated that TwGGPPS1 was similar to GGPPS from other species of plants. For the first time the cloning of geranylgeranyl diphosphate synthase gene from T. wilfordii was reported, it lays the foundation for further research of diterpenoids biosynthetic pathway.
Amino Acid Sequence ; Cloning, Molecular ; Farnesyltranstransferase ; chemistry ; genetics ; metabolism ; Molecular Sequence Data ; Phylogeny ; Plant Proteins ; chemistry ; genetics ; metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Tripterygium ; chemistry ; enzymology ; genetics