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PubMed2005

Methods for obtaining and analyzing whole chloroplast genome sequences.

During the past decade, there has been a rapid increase in our understanding of plastid genome organization and evolution due to the availability of many new completely sequenced genomes. There are 45 complete genomes published and ongoing projects are likely to increase this sampling to nearly 200 genomes during the next 5 years. Several groups of researchers including ours have been developing new techniques for gathering and analyzing entire plastid genome sequences and details of these developments are summarized in this chapter. The most important developments that enhance our ability to generate whole chloroplast genome sequences involve the generation of pure fractions of chloroplast genomes by whole genome amplification using rolling circle amplification, cloning genomes into Fosmid or bacterial artificial chromosome (BAC) vectors, and the development of an organellar annotation program (Dual Organellar GenoMe Annotator [DOGMA]). In addition to providing details of these methods, we provide an overview of methods for analyzing complete plastid genome sequences for repeats and gene content, as well as approaches for using gene order and sequence data for phylogeny reconstruction. This explosive increase in the number of sequenced plastid genomes and improved computational tools will provide many insights into the evolution of these genomes and much new data for assessing relationships at deep nodes in plants and other photosynthetic organisms.

Amino Acid Sequence↗
PubMed1998

Differentiation of necrotizing fasciitis and cellulitis using MR imaging.

OBJECTIVE: This study was performed to evaluate the diagnostic value of MR imaging in differentiating necrotizing fasciitis from cellulitis. MATERIALS AND METHODS: Spin-echo T1-weighted, T2-weighted, and contrast-enhanced T1-weighted spin-echo sequences were performed in 15 patients with clinically suspected necrotizing fasciitis. In two other patients, only unenhanced imaging was performed. The MR imaging results were correlated with the surgical findings in 11 cases, with autopsy in one case, and with the clinical outcome in five cases. RESULTS: Cellulitis was diagnosed when subcutaneous thickening with fluid collections was revealed on T2-weighted images and when subcutaneous tissue or superficial fascia or both showed contrast enhancement. For the diagnosis of necrotizing fasciitis, imaging revealed additional involvement of deep fasciae with fluid collections, thickening, and enhancement after contrast administration. According to these criteria, we found 11 cases of necrotizing fasciitis and six of cellulitis. MR imaging identified all 11 cases of necrotizing fasciitis correctly when compared with the surgical findings. One false-positive case of cellulitis was overstaged and was thought to be necrotizing fasciitis. Contrast-enhanced T1-weighted sequences delineated abscesses and areas of necrosis more clearly than T2-weighted sequences did, but showed no additional lesions. CONCLUSION: When no deep fascial involvement is revealed with MR imaging, necrotizing fasciitis can be excluded. However, because its sensitivity exceeds its specificity, MR imaging tends to overestimate the extent of deep fascial involvement. Therefore, the therapeutic regimen should be based on a combination of clinical findings and MR imaging.

Adult↗
PubMed1999

Three-dimensional phase contrast MR cerebral venography with zero filling interpolation in the slice encoding direction.

The purpose of this study was to evaluate the magnetic resonance (MR) cerebral venography findings of a three-dimensional phase contrast MR sequence with zero filling interpolation of the data in the slice encoding direction. Fifty volunteers were enrolled in the study. Images were obtained on a 1.5 MR imaging system with acquisition time of 12 min. MIP images were reconstructed throughout the entire imaging volume. A grading scale system was used to assess dural venous sinuses, major deep veins, cortical, and cortical eponymic veins. Inferior group of dural venous sinuses, inferior sagittal sinus, and cortical eponymic veins were poorly demonstrated. Score of the superior sagittal sinus, the straight sinus, the confluence of the superior sinus group, the right transverse and sigmoid sinuses, the internal veins, and the vein of Galen was excellent. The score of the left transverse and sigmoid sinuses was good. In conclusion, when using zero filling interpolation of the data in a three-dimensional phase contrast MR cerebral venography sequence, the superior group of dural venous sinuses and main major deep veins are demonstrated with good conspicuity.

Adolescent↗
PubMed2006

The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features.

BACKGROUND: Sequence data and other characters from mitochondrial genomes (gene translocations, secondary structure of RNA molecules) are useful in phylogenetic studies among metazoan animals from population to phylum level. Moreover, the comparison of complete mitochondrial sequences gives valuable information about the evolution of small genomes, e.g. about different mechanisms of gene translocation, gene duplication and gene loss, or concerning nucleotide frequency biases. The Peracarida (gammarids, isopods, etc.) comprise about 21,000 species of crustaceans, living in many environments from deep sea floor to arid terrestrial habitats. Ligia oceanica is a terrestrial isopod living at rocky seashores of the european North Sea and Atlantic coastlines. RESULTS: The study reveals the first complete mitochondrial DNA sequence from a peracarid crustacean. The mitochondrial genome of Ligia oceanica is a circular double-stranded DNA molecule, with a size of 15,289 bp. It shows several changes in mitochondrial gene order compared to other crustacean species. An overview about mitochondrial gene order of all crustacean taxa yet sequenced is also presented. The largest non-coding part (the putative mitochondrial control region) of the mitochondrial genome of Ligia oceanica is unexpectedly not AT-rich compared to the remainder of the genome. It bears two repeat regions (4x 10 bp and 3x 64 bp), and a GC-rich hairpin-like secondary structure. Some of the transfer RNAs show secondary structures which derive from the usual cloverleaf pattern. While some tRNA genes are putative targets for RNA editing, trnR could not be localized at all. CONCLUSION: Gene order is not conserved among Peracarida, not even among isopods. The two isopod species Ligia oceanica and Idotea baltica show a similarly derived gene order, compared to the arthropod ground pattern and to the amphipod Parhyale hawaiiensis, suggesting that most of the translocation events were already present the last common ancestor of these isopods. Beyond that, the positions of three tRNA genes differ in the two isopod species. Strand bias in nucleotide frequency is reversed in both isopod species compared to other Malacostraca. This is probably due to a reversal of the replication origin, which is further supported by the fact that the hairpin structure typically found in the control region shows a reversed orientation in the isopod species, compared to other crustaceans.

Animals↗
PubMed2004

Dynamics of a human interparalog gene conversion hotspot.

Gene conversion between paralogs can alter their patterns of sequence identity, thus obscuring their evolutionary relationships and affecting their propensity to sponsor genomic rearrangements. The details of this important process are poorly understood in the human genome because allelic diversity complicates the interpretation of interparalog sequence differences. Here we exploit the haploid nature of the Y chromosome, which obviates complicating interallelic processes, together with its known phylogeny, to understand the dynamics of conversion between two directly repeated HERVs flanking the 780-kb AZFa region on Yq. Sequence analysis of a 787-bp segment of each of the HERVs in 36 Y chromosomes revealed one of the highest nucleotide diversities in the human genome, as well as evidence of a complex patchwork of highly directional gene conversion events. The rate of proximal-to-distal conversion events was estimated as 2.4 x 10(-4) to 1.2 x 10(-3) per generation (3.9 x 10(-7) to 1.9 x 10(-6) per base per generation), and the distal-to-proximal rate as about one-twentieth of this. Minimum observed conversion tract lengths ranged from 1 to 158 bp and maximum lengths from 19 to 1365 bp, with an estimated mean of 31 bp. Analysis of great ape homologs shows that conversion in this hotspot has a deep evolutionary history.

Animals↗
PubMedDate not supplied

The deep infrapatellar bursa: prevalence and morphology on routine magnetic resonance imaging of the knee.

OBJECTIVE: To evaluate the presence, location, and dimensions of the deep infrapatellar bursa on routine magnetic resonance (MR) imaging of the knee. METHODS: The study group consisted of 213 knees in 204 consecutive individuals who had undergone routine MR imaging examination of the knee within a 365-day period. Magnetic resonance examinations consisted of T1-, proton-density-, and T2-weighted sagittal; spectral presaturation inversion recovery coronal; and T2*-weighted transverse sequences. Exclusion criteria were previous knee arthroscopy or surgery or the presence of a mass lesion infiltrating the infrapatellar fat pad. The presence, location, and dimensions of the deep infrapatellar bursa were studied. The bursa was also analyzed with regard to knee joint synovial effusion (absent, mild, or marked). RESULTS: The deep infrapatellar bursa was detected in 68% of the knees, most commonly on the lateral paramedian sagittal MR images. There was no statistically significant difference between male and female subjects or between the knee sides with regard to the detection of the deep infrapatellar bursa (P > 0.05). No correlation was found between synovial effusion and the presence of the deep infrapatellar bursa. The mean anteroposterior and craniocaudal dimensions of the deep infrapatellar bursa on sagittal T2-weighted MR images were 2.1-2.7 mm and 7.3-9.1 mm, respectively, on its lateral, central, or medial location within the sagittal MR image stack. CONCLUSION: An awareness of the dimensions and location of the deep infrapatellar bursa is important in distinguishing it from pathologic lesions (eg, bursitis).

Adolescent↗
PubMed2025

Soffritto: a deep learning model for predicting high-resolution replication timing.

MOTIVATION: Replication timing (RT) refers to the order in which DNA loci are replicated during S phase. RT is cell-type specific and implicated in cellular processes including transcription, differentiation, and disease. RT is typically quantified genome-wide using two-fraction assays (e.g. Repli-Seq) which sort cells into early and late S phase fractions followed by DNA sequencing, yielding a ratio as the RT signal. While two-fraction RT data are widely available in multiple cell lines, it is limited in its ability to capture high-resolution RT features. To address this, high-resolution Repli-Seq, which quantifies RT across 16 fractions, was developed, but it is costly and technically challenging with very limited data generated to date. RESULTS: Here, we developed Soffritto, a deep learning model that predicts high-resolution RT data using two-fraction RT data, histone ChIP-seq data, GC content, and gene density as input. Soffritto is composed of a Long Short-Term Memory (LSTM) module and a prediction module. The LSTM module learns long- and short-range interactions between genomic bins, while the prediction module is composed of a fully connected layer that outputs a 16-fraction probability vector for each bin using the LSTM module's embeddings as input. By performing both within cell line and cross-cell line training and testing for five human and mouse cell lines, we show that Soffritto is able to capture experimental 16-fraction RT signals with high accuracy, and the predicted signals allow detection of high-resolution RT patterns. AVAILABILITY AND IMPLEMENTATION: Soffritto is available at https://github.com/ay-lab/Soffritto.

Deep Learning↗
PubMed1992

Is Pneumocystis carinii a deep mycosis-like agent?

Pneumocystis carinii is a widespread eukaryotic microorganism found in the lungs of healthy mammals, including humans. It is able to proliferate extensively in the alveoli, becoming an important agent of severe pneumonitis in immunosuppressed hosts, especially in persons suffering from AIDS. The taxonomic position of P. carinii is uncertain. Typical cytoplasmic organelles of eukaryotic cells have been found and described in the parasite. Biochemical research is hindered by the lack of an efficient in vitro culture system. Results of comparative study of nucleic acid sequences suggest that Pneumocystis is a fungus. However, ultrastructural, biochemical and nucleic acid homology insights appear as clearly insufficient to class Pneumocystis. Pneumocystis infection might be acquired, as deep mycoses, from environmental sources through the respiratory tract. Thus, the hypothesis of an environmental stage of the parasite must be considered. Pneumocystis might be seen as a widespread pathogenic dimorphous fungus. As fungal agents, P. carinii is able to disseminate from the infected lung to other organs. However, deep mycoses and pneumocystosis induce different histopathological changes in the host. Furthermore, deep fungal infections, unlike pneumocystosis, cannot be transmitted from one infested host to another one. Beside these two aspects, pneumocystosis shares many features with deep mycoses. Research on the epidemiology of pneumocystosis is needed.

Animals↗
PubMed1995

[MRI aspects of progressive multifocal leukoencephalopathy].

Progressive Multifocal Leukoencephalopathy is a demyelinating disease. MRI shows high signal intensity areas on T2w sequence and low intensity aeras on T1w sequence, without enhancement after intravenous contrast injection. The involvement of arcuate fiber (U fibers) creates a sharp border with the cortex. There is no mass effect. Involvement of parieto-occipital areas is frequent. The lesions may be uni or bilateral, single or multiple; bilateral lesions are asymmetric. This typical appearance on MR images occurs in 90% of the patients with PML. Some atypical patterns may occur: focal hemorrhage, atrophy, faint peripheral enhancement and involvement of deep gray matter (basal ganglia). In most cases, the clinical and MR features provide the diagnosis. The main differential diagnosis, in MRI, is HIV-leukoencephalitis, but lesions are diffuse, less intense on T2w sequence and not visible on T1, without involvement of the arcuate fibers. Stereotactic biopsy should be performed only for atypical lesions, particularly in case of predominant involvement of deep gray structures.

AIDS Dementia Complex↗
PubMed2005

Characterization of a deep-sea microbial mat from an active cold seep at the Milano mud volcano in the Eastern Mediterranean Sea.

A white, filamentous microbial mat at the Milano mud volcano in the Eastern Mediterranean Sea was sampled during the Medinaut cruise of the R/V Nadir in 1998. The composition of the mat community was characterized using a combination of phylogenetic and lipid biomarker methods. The mat sample was filtered through 0.2 and 5-microm filters to coarsely separate unicellular and filamentous bacteria. Analyses of 16S rRNA gene sequences amplified from the total community DNA from these fractions showed that similar archaeal populations were present in both fractions. However, the bacterial populations in the fractions differed from one another, and were more diverse than the archaeal ones. Lipid analysis showed that bacteria were the dominant members of the mat microbial community and the relatively low delta(13)C carbon isotope values of bulk bacterial lipids suggested the occurrence of methane- and sulfide-based chemo(auto)trophy. Consistent with this, the bacterial populations in the fractions were related to Alpha-, Gamma- and Epsilonproteobacteria, most of which were chemoautotrophic bacteria that utilize hydrogen sulfide (or reduced sulfur compounds) and/or methane. The most common archaeal 16S rRNA gene sequences were related to those of previously identified Archaea capable of anaerobic methane oxidation. Although the filamentous organisms observed in the mat were not conclusively identified, our results indicated that the Eastern Mediterranean deep-sea microbial mat community might be sustained on a combination of methane- and sulfide-driven chemotrophy.

Archaea↗
PubMed1999

Acute swelling of the limbs: magnetic resonance pictorial review of fascial and muscle signal changes.

OBJECTIVE: This pictorial review analyzes the magnetic resonance (MR) fascial/muscular changes in 69 patients referred as emergencies with acute swelling of the limbs (ASL) from various causes. METHODS AND MATERIAL: A prospective MR imaging (MRI) study of 69 patients referred as emergencies for ASL was performed. Our population consisted of 45 patients with skin and soft-tissue infections (cellulitis and necrotizing fasciitis, and pyomyositis), six patients with soft-tissue inflammatory diseases (dermatomyositis, graft-versus-host disease), 11 patients with acute deep venous thrombosis, three patients with rhabdomyolysis, one patient with acute denervation and three other patients with rare diseases. Hematomas, tumorous or infectious bone involvement and soft-tissue tumors were excluded. All studies included spin echo T1-weighted images and spin echo T2-weighted images. Gadolinium-enhanced spin echo T1-weighted images were obtained when an abscess was suspected on T2-weighted images. Selective fat-saturated T1- and T2-weighted sequences were also used. MRI analysis was performed to obtain a compartmentalized anatomical approach according to the location of signal abnormalities in subcutaneous fat, superficial and deep fascia and muscle. RESULTS: In all patients with ASL, MRI demonstrated soft-tissue abnormalities involving subcutaneous fat, superficial fascia, deep fascia, or muscle. Although MR findings were non-specific, MRI appears sensitive for detecting subtle fascial and muscle signal changes. CONCLUSIONS: In skin and soft-tissue infections, MRI can be helpful for therapeutic management by determining the depth of soft-tissue involvement, particularly within fasciae and muscles, which is partly related to the severity of cellulitis with severe systemic manifestations. MRI can also aid the surgeon in diagnosing abscesses. In inflammatory diseases, MRI can determine the best site for biopsy and also monitor therapeutic response.

Adolescent↗
PubMed2006

Presence of Hydrogenophilus thermoluteolus DNA in accretion ice in the subglacial Lake Vostok, Antarctica, assessed using rrs, cbb and hox.

The 3561 m Vostok ice core sample originating from the subglacial Lake Vostok accretion (frozen lake water) ice with sediment inclusions was thoroughly studied by various means to confirm the presence of the thermophile bacterium Hydrogenophilus thermoluteolus reported earlier in the 3607 m accretion ice sample. PCR and molecular-phylogenetic analyses performed in two independent laboratories were made using different 16S rRNA gene (rrs) targeted primers. As a result, rrs-targeted PCR permitted to recover several very closely related clones with a small genetic distance to Hydrogenophilus thermoluteolus (< 1%). In addition, RubisCO (cbbL or rbcL) and NiFe-Hydrogenase (hoxV or hupL) targeted PCR have also allowed to recover sequences highly related to Hydrogenophilus thermoluteolus. All these results point to the presence of thermophilic chemoautotrophic microorganisms in Lake Vostok accretion ice. They presumably originate from deep faults in the bedrock cavity containing the lake in which episodes of seismotectonic activity would release debris along with microbial cells.

Antarctic Regions↗
PubMed1990

Molecular analysis of deep-subsurface bacteria.

Bacterial isolates from deep-sediment samples from three sites at the Savannah River site, near Aiken, S.C., were studied to determine their microbial community composition and DNA structure by using total DNA hybridization and moles percent G + C. Standard phenotypic identification underestimated the bacterial diversity at the three sites, since isolates with the same phenotype had different DNA structures in terms of moles percent G + C and DNA homology. The G + C content of deep-subsurface bacteria ranged from 20 to 77 mol%. More than 60% of the isolates tested had G + C values similar to those of Pseudomonas spp., and 12% had values similar to those of Acinetobacter spp. No isolates from deeper formations showed the same DNA composition as isolates from upper formations. Total-DNA hybridization and DNA base composition analysis provided a better resolution than phenotypic tests for the understanding of the diversity and structure of deep-subsurface bacterial communities. On the basis of the moles percent G + C values, deep-subsurface isolates tested seemed to belong to the families Pseudomonadaceae and Neisseriaceae, which might reflect a long period of adaptation to the environmental conditions of the deep subsurface.

Bacteria↗
PubMed1995

Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.

Sequence-dependent bending of the helical axes in 112 oligonucleotide duplex crystal structures resident in the Nucleic Acid Database have been analyzed and compared with the use of bending dials, a computer graphics tool. Our analysis includes structures of both A and B forms of DNA and considers both uncomplexed forms of the double helix as well as those bound to drugs and proteins. The patterns in bending preferences in the crystal structures are analyzed by base pair steps, and emerging trends are noted. Analysis of the 66 B-form structures in the Nucleic Acid Database indicates that uniform trends within all pyrimidine-purine and purine-pyrimidine steps are not necessarily observed but are found particularly at CG and GC steps of dodecamers. The results support the idea that AA steps are relatively straight and that larger roll bends occur at or near the junctions of these A-tracts with their flanking sequences. The data on 16 available crystal structures of protein-DNA complexes indicate that the majority of the DNA bends induced via protein binding are sharp localized kinks. The analysis of the 30 available A-form DNA structures indicates that these structures are also bent and show a definitive preference for bending into the deep major groove over the shallow minor groove.

Base Sequence↗
PubMed2006

Recombination between elongation factor 1alpha genes from distantly related archaeal lineages.

Homologous recombination (HR) and lateral gene transfer are major processes in genome evolution. The combination of the two processes, HR between genes in different species, has been documented but is thought to be restricted to very similar sequences in relatively closely related organisms. Here we report two cases of interspecific HR in the gene encoding the core translational protein translation elongation factor 1alpha (EF-1alpha) between distantly related archaeal groups. Maximum-likelihood sliding window analyses indicate that a fragment of the EF-1alpha gene from the archaeal lineage represented by Methanopyrus kandleri was recombined into the orthologous gene in a common ancestor of the Thermococcales. A second recombination event appears to have occurred between the EF-1alpha gene of the genus Methanothermobacter and its ortholog in a common ancestor of the Methanosarcinales, a distantly related euryarchaeal lineage. These findings suggest that HR occurs across a much larger evolutionary distance than generally accepted and affects highly conserved essential "informational" genes. Although difficult to detect by standard whole-gene phylogenetic analyses, interspecific HR in highly conserved genes may occur at an appreciable frequency, potentially confounding deep phylogenetic inference and hypothesis testing.

Archaea↗
PubMed2003

Phylogeography of the harlequin beetle-riding pseudoscorpion and the rise of the Isthmus of Panamá.

Molecular and geological evidence indicates that the emergence of the Isthmus of Panamá influenced the historical biogeography of the Neotropics in a complex, staggered manner dating back at least 9 Myr bp. To assess the influence of Isthmus formation on the biogeography of the harlequin beetle-riding pseudoscorpion, Cordylochernes scorpioides, we analysed mitochondrial COI sequence data from 71 individuals from 13 locations in Panamá and northern South America. Parsimony and likelihood-based phylogenies identified deep divergence between South American and Panamanian clades. In contrast to low haplotype diversity in South America, the Panamanian Cordylochernes clade is comprised of three highly divergent lineages: one clade consisting predominantly of individuals from central Panamá (PAN A), and two sister clades (PAN B1 and PAN B2) of western Panamanian pseudoscorpions. Breeding experiments demonstrated a strictly maternal mode of inheritance, indicating that our analyses were not confounded by nuclear-mitochondrial pseudogenes. Haplotype diversity is striking in western Atlantic Panamá, where all three Panamanian clades can occur in a single host tree. This sympatry points to the existence of a cryptic species hybrid zone in western Panamá, a conclusion supported by interclade crosses and coalescence-based migration rates. Molecular clock estimates yield a divergence time of approximately 3 Myr between the central and western Panamanian clades. Taken together, these results are consistent with a recent model in which a transitory proto-Isthmus enabled an early wave of colonization out of South America at the close of the Miocene, followed by sea level rise, inundation of the terrestrial corridor and then a second wave of colonization that occurred when the Isthmus was completed approximately 3 Myr bp.

Animal Migration↗
PubMed1989

Angiogenesis on the optic tectum of albino Xenopus laevis tadpoles.

Developing blood vessels were observed directly on the dorsal surface of the optic tectum of anesthetized, transparent albino Xenopus laevis tadpoles, stages 41-54. Case histories of individual tadpoles indicated that pial capillaries developed by the classical mechanism of sprouting of endothelial cells from existing blood vessels. 'Deep sources' appeared on the tectal surface during development. These were sites of upwelling blood cells from capillaries within the nervous tissue of the tectum into vessels on the surface. Few 'deep sinks' were observed in the dorsal tectum of normal tadpoles. The earliest deep sources were probably formed by sprouts from the surface vessels through the basement membrane and into the nervous tissue; later ones may also have formed from internal sprouts back to the surface. Maps of deep sources and of surface vessels in case histories indicated that neural tissue and blood vessels in the caudal half of the tectum grew faster than in the rostral half. The medial venules on the dorsal tectum originated as ordinary-sized rostrocaudal capillaries. They enlarged in diameter as they drained the increasing flow of blood from the tectum into the choroid plexus over the 4th ventricle. Some capillaries disappeared or regressed during development. Our observations on the tectum were consistent with the classical sequence of loss of flow, narrowing, collapse of the lumen, and retraction of endothelial cells into adjacent vessels. Likely sites for regression were upstream from a deep source and at crosslinks between transverse vessels on the lateral tectum. Morphometric parameters for tectal angiogenesis were (a) surface density (mm-1) calculated as total length of surface vessels divided by the dorsally projected surface area, and (b) density of deep sources (mm-2) calculated as total number divided by surface area. From stages 41/42 to 50 average surface density approximately doubled, and average density of deep sources increased about 5-fold. Some of the factors which might be expected to alter brain angiogenesis include nervous activity, availability of O2, and metabolic rate. Removal of one eye deprived the contralateral tectum of direct retinal inputs, while the ipsilateral side was a control in the same animal. Anterograde labeling of retinal axons with diI18 from the remaining eye confirmed projections only to the opposite side. No significant differences in densities of surface vessels or of deep sources were observed between the contralateral and ipsilateral sides of the tectum.(ABSTRACT TRUNCATED AT 400 WORDS)

Aging↗
PubMed2003

The crystal structure of shikimate dehydrogenase (AroE) reveals a unique NADPH binding mode.

Shikimate dehydrogenase catalyzes the NADPH-dependent reversible reduction of 3-dehydroshikimate to shikimate. We report the first X-ray structure of shikimate dehydrogenase from Haemophilus influenzae to 2.4-A resolution and its complex with NADPH to 1.95-A resolution. The molecule contains two domains, a catalytic domain with a novel open twisted alpha/beta motif and an NADPH binding domain with a typical Rossmann fold. The enzyme contains a unique glycine-rich P-loop with a conserved sequence motif, GAGGXX, that results in NADPH adopting a nonstandard binding mode with the nicotinamide and ribose moieties disordered in the binary complex. A deep pocket with a narrow entrance between the two domains, containing strictly conserved residues primarily contributed by the catalytic domain, is identified as a potential 3-dehydroshikimate binding pocket. The flexibility of the nicotinamide mononucleotide portion of NADPH may be necessary for the substrate 3-dehydroshikimate to enter the pocket and for the release of the product shikimate.

Alcohol Oxidoreductases↗