-
[show abstract]
[hide abstract]
ABSTRACT: Phosphoglucose isomerase (PGI) is a key enzyme in glycolysis and glycogenesis that catalyses the interconversion of glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P). For crystallographic studies, PGI from the human malaria parasite Plasmodium falciparum (PfPGI) was overproduced in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data to 1.5 A resolution were collected from an orthorhombic crystal form belonging to space group P2(1)2(1)2(1) with unit-cell parameters a = 103.3, b = 104.1, c = 114.6 A. Structural analysis by molecular replacement is in progress.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 03/2010; 66(Pt 3):333-6. · 0.51 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Pig heart peroxisomal carbonyl reductase (PerCR) belongs to the short-chain dehydrogenase/reductase family, and its sequence comprises a C-terminal SRL tripeptide, which is a variant of the type 1 peroxisomal targeting signal (PTS1) Ser-Lys-Leu. PerCR is imported into peroxisomes of HeLa cells when the cells are transfected with vectors expressing the enzyme. However, PerCR does not show specific targeting when introduced into the cells with a protein transfection reagent. To understand the structural basis for peroxisomal localization of PerCR, we determined the crystal structure of PerCR. Our data revealed that the C-terminal PTS1 of each subunit of PerCR was involved in intersubunit interactions and was buried in the interior of the tetrameric molecule. These findings indicate that the PTS1 receptor Pex5p in the cytosol recognizes the monomeric form of PerCR whose C-terminal PTS1 is exposed, and that this PerCR is targeted into the peroxisome, thereby forming a tetramer.
Structure 04/2008; 16(3):388-97. · 6.35 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Pig heart carbonyl reductase (PHCR), which belongs to the short-chain dehydrogenase/reductase (SDR) family, has been crystallized by the hanging-drop vapour-diffusion method. Two crystal forms (I and II) have been obtained in the presence of NADPH. Form I crystals belong to the tetragonal space group P4(2), with unit-cell parameters a = b = 109.61, c = 94.31 A, and diffract to 1.5 A resolution. Form II crystals belong to the tetragonal space group P4(1)2(1)2, with unit-cell parameters a = b = 120.10, c = 147.00 A, and diffract to 2.2 A resolution. Both crystal forms are suitable for X-ray structure analysis at high resolution.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 11/2006; 62(Pt 10):1037-40. · 0.51 Impact Factor
-
Tadashi Baba,
Fumihiko Takeuchi,
Makoto Kuroda,
Harumi Yuzawa, Ken-ichi Aoki,
Akio Oguchi,
Yoshimi Nagai,
Natsuko Iwama,
Kazuyuki Asano,
Timothy Naimi,
Hiroko Kuroda,
Longzhu Cui,
Kenji Yamamoto,
Keiichi Hiramatsu
[show abstract]
[hide abstract]
ABSTRACT: THE LANCET • Vol 359 • May 25, 2002 • www.thelancet.com 1819 Summary Background A new type of meticillin-resistant Staphylococcus aureus (MRSA), designated community-acquired MRSA, is becoming increasingly noticeable in the community, some strains of which cause fatal infections in otherwise healthy individuals. By contrast with hospital-acquired MRSA, community-acquired MRSA is more susceptible to non -lactam antibiotics. We investigated the high virulence potential of certain strains of this bacterium. Methods We ascertained the whole genome sequence of MW2, a strain of community-acquired MRSA, by shotgun cloning and sequencing. MW2 caused fatal septicaemia and septic arthritis in a 16-month-old girl in North Dakota, USA, in 1998. The genome of this strain was compared with those of hospital-acquired MRSA strains, including N315 and Mu50. Findings Meticillin resistance gene (mecA) in MW2 was carried by a novel allelic form (type IVa) of staphylococcal cassette chromosome mec (SCCmec), by contrast with type II in N315 and Mu50. Type IVa SCCmec did not carry any of the multiple antibiotic resistance genes reported in type II SCCmec. By contrast, 19 additional virulence genes were recorded in the MW2 genome. All but two of these virulence genes were noted in four of the seven genomic islands of MW2. Interpretation MW2 carried a range of virulence and resistance genes that was distinct from those displayed on the chromosomes of extant S aureus strains. Most genes were carried by specific allelic forms of genomic islands in the MW2 chromosome. The combination of allelic forms of genomic islands is the genetic basis that determines the pathogenicity of medically important phenotypes of S aureus, including those of community-acquired MRSA strains.
The Lancet 01/2002; 359:1819--27. · 38.28 Impact Factor
-
Masayuki Machida,
Shuji Yamazaki,
Sumiko Kunihiro,
Toshihiro Tanaka,
Norihiro Kushida,
Kouji Jinnno,
Yuji Haikawa,
Jun Yamazaki,
Saori Yamamoto,
Mitsuo Sekine,
Akio Oguchi,
Yoshimi Nagai,
Mari Sakai, Ken-ichi Aoki,
Keiko Ogura,
Yutaka Kudoh,
Hisashi Kikuchi,
Michael Q. Zhang,
Mitsuhiro Yanagida
[show abstract]
[hide abstract]
ABSTRACT: A genomic 38 kbp segment on the c1750 cosmid clone containing the cdc2 gene, located in the left arm of chromosome II from Schizosaccharomyces pombe, was sequenced. The segment was found to have five previously known genes, pht1, cdc2, his3, act1 and mei4. Among 11 coding sequences (CDSs) predicted by the gene finding software INTRON.PLOT., four CDSs, pi007, pi010, pi014 and pi016, had considerable similarity to 40S ribosomal protein, glycosyltransferase, cdc2-related protein kinase and α-1,2-mannosyltransferase, respectively. Another unusually huge open reading frame (ORF) (pi011), consisting of 2233 amino acids, existed, having significant homology to α-amylase, granule-bound glycogen synthase and the Sz. pombe YS 1110 clone product at the N-terminal, middle and C-terminal regions, respectively. All the predicted 11 CDSs were experimentally analysed by RACE PCR. The sequencing of the RACE products revealed that there were two small overlaps at the 3′ untranslated regions (UTRs) between pi004 and pi005 (17 bp) and between pi007 and pi008 (2 bp). The distances between 5′ end of the 5′UTR and the putative translation initiation codon varied from 10 to 302 nucleotides (nt) among the nine CDSs successfully analysed by 5′-RACE. The expression level of each CDS on this clone was determined. Among the 16 genes on this clone, the previously determined genes, pht1, cdc2, his3 and act1, were found to be most highly expressed. Finally, cDNAs of all the newly identified genes were detected by RACE, proving the actual expression of these genes. The nucleotide sequence has been submitted to the EMBL database under Accession No. AB004534. Copyright © 2000 John Wiley & Sons, Ltd.
Yeast 02/2000; 16(1):71 - 80. · 1.89 Impact Factor
-
Yutaka Kawarabayasi,
Mituhiro Sawada,
Hiroshi Horikawa,
Yuji Haikawa,
Yumi Hino,
Saori Yamamoto,
Mitsuo Sekine,
Sin-ichi Baba,
Hiroki Kosugi,
Akira Hosoyama, [......],
Norihiro Kushida,
Akio Oguchi, Ken-ichi Aoki,
Takio Yoshizawa,
Yoshinobu Nakamura,
Frank T. Robb,
Koki Horikoshi,
Yaeko Masuchi,
Hiroaki Shizuya,
Hisasi Kikuchi
[show abstract]
[hide abstract]
ABSTRACT: The complete sequence of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3, has been determined by assembling the sequences of the physical map-based contigs of fosmid clones and of long polymerase chain reaction (PCR) products which were used for gap-filling. The entire length of the genome was 1,738,505 bp. The authenticity of the entire genome sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA. As the potential protein-coding regions, a total of 2061 open reading frames (ORFs) were assigned, and by similarity search against public databases, 406 (19.7%) were related to genes with putative function and 453 (22.0%) to the sequences registered but with unknown function. The remaining 1202 ORFs (58.3%) did not show any significant similarity to the sequences in the databases. Sequence comparison among the assigned ORFs in the genome provided evidence that a considerable number of ORFs were generated by sequence duplication. By similarity search, 11 ORFs were assumed to contain the intein elements. The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA genes and 46 tRNA genes including two with the intron structure. All the assigned ORFs and RNA coding regions occupied 91.25% of the whole genome. The data presented in this paper are available on the internet at http://www.nite.go.jp .
DNA Research 05/1998; · 5.16 Impact Factor
-
Yutaka Kawarabayasi,
Mituhiro Sawada,
Hiroshi Horikawa,
Yuji Haikawa,
Yumi Hino,
Saori Yamamoto,
Mitsuo Sekine,
Sin-ichi Baba,
Hiroki Kosugi,
Akira Hosoyama, [......],
Norihiro Kushida,
Akio Oguchi, Ken-ichi Aoki,
Takio Yoshizawa,
Yoshinobu Nakamura,
Frank T. Robb,
Koki Horikoshi,
Yaeko Masuchi,
Hiroaki Shizuya,
Hisasi Kikuchi
-
Yutaka Kawarabayasi,
Yumi Hino,
Hiroshi Horikawa,
Koji Jin-no,
Mikio Takahashi,
Mitsuo Sekine,
Sin-ichi Baba,
Akiho Ankai,
Hiroki Kosugi,
Akira Hosoyama, [......],
Jun Yamazaki,
Norihiro Kushida,
Akio Oguchi, Ken-ichi Aoki,
Sayaka Masuda,
Masao Yanagii,
Masami Nishimura,
Akihiko Yamagishi,
Tairo Oshima,
Hisasi Kikuchi
[show abstract]
[hide abstract]
ABSTRACT: The complete genomic sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7 which optimally grows at 80°C, at low pH, and under aerobic conditions, has been determined by the whole genome shotgun method with slight modifications. The genomic size was 2,694,756 bp long and the G+C content was 32.8%. The following RNA-coding genes were identified: a single 16S–23S rRNA cluster, one 5S rRNA gene and 46 tRNA genes (including 24 intron-containing tRNA genes). The repetitive sequences identified were SR-type repetitive sequences, long dispersed-type repetitive sequences and Tn-like repetitive elements. The genome contained 2826 potential protein-coding regions (open reading frames, ORFs). By similarity search against public databases, 911 (32.2%) ORFs were related to functional assigned genes, 921 (32.6%) were related to conserved ORFs of unknown function, 145 (5.1%) contained some motifs, and remaining 849 (30.0%) did not show any signi.cant similarity to the registered sequences. The ORFs with functional assignments included the candidate genes involved in sulfide metabolism, the TCA cycle and the respiratory chain. Sequence comparison provided evidence suggesting the integration of plasmid, rearrangement of genomic structure, and duplication of genomic regions that may be responsible for the larger genomic size of the S. tokodaii strain7 genome. The genome contained eukaryote-type genes which were not identified in other archaea and lacked the CCA sequence in the tRNA genes. The result suggests that this strain is closer to eukaryotes among the archaea strains so far sequenced. The data presented in this paper are also available on the internet homepage ( http://www.bio.nite.go.jp/E-home/genome_list-e.html/ ).
