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At least 1,693 records · Page 94Linked to original sources
PubMed2004

Surfactant protein A, an innate immune factor, is expressed in the vaginal mucosa and is present in vaginal lavage fluid.

Surfactant protein A (SP-A), first identified as a component of the lung surfactant system, is now recognized to be an important contributor to host defence mechanisms. SP-A can facilitate phagocytosis by opsonizing bacteria, fungi and viruses, stimulate the oxidative burst by phagocytes and modulate pro-inflammatory cytokine production by phagocytic cells. SP-A can also provide a link between innate and adaptive immune responses by promoting differentiation and chemotaxis of dendritic cells. Because of the obvious relevance of these mechanisms to the host defence and 'gate keeping' functions of the lower genital tract, we examined human vaginal mucosa for SP-A protein and transcripts and analysed vaginal lavage fluid for SP-A. By immunocytochemistry, SP-A was identified in two layers of the vaginal epithelium: the deep intermediate layer (the site of newly differentiated epithelial cells); and the superficial layer (comprising dead epithelial cells), where SP-A is probably extracellular and associated with a glycocalyx. Transcripts of SP-A were identified by Northern blot analysis in RNA isolated from vaginal wall and shown, by sequencing of reverse transcription-polymerase chain reaction products, to be derived from each of the two closely related SP-A genes, SP-A1 and SP-A2. SP-A was identified in vaginal lavage fluid by two-dimensional gel electrophoresis, and confirmed by mass spectrometry. This study provides evidence, for the first time, that SP-A is produced in a squamous epithelium, namely the vaginal mucosa, and has a localization that would allow it to contribute to both the innate and adaptive immune response. The findings support the hypothesis that in the vagina, as in lung, SP-A is an essential component of the host-defence system. A corollary hypothesis is that qualitative and quantitative alterations of normal SP-A may play a role in the pathogenesis of lower genital tract inflammatory conditions.

Adult↗
PubMed1994

Genetic and biochemical analyses of the biosynthesis of the yellow carotenoid 4,4'-diaponeurosporene of Staphylococcus aureus.

The major pigment produced by Staphylococcus aureus Newman is the deep-yellow carotenoid 4,4'-diaponeurosporene; after prolonged cultivation, this pigment is in part converted to the orange end product staphyloxanthin. From this strain a 3.5-kb DNA fragment was identified which after being cloned into Escherichia coli and Staphylococcus carnosus conferred the ability to produce 4,4'-diaponeurosporene. DNA sequencing of this fragment revealed two open reading frames (ORFs) which are very likely cotranscribed. ORF1 encodes a 254-amino-acid hydrophobic protein, CrtM (M(r), 30,121). The deduced sequence of CrtM exhibits in three domains similarities to the sequences of Saccharomyces cerevisiae and human squalene synthases and phytoene synthases of various bacteria. ORF2 encodes a 448-amino-acid hydrophobic protein, CrtN, with an M(r) of 50,853 whose deduced sequence is similar to those of phytoene desaturases of other bacteria. At the N terminus of CrtN a classical FAD-, NAD(P)-binding domain is found. Spectrophotometry and gas chromatography-mass spectrometry analyses of the carotenoid production of E. coli and S. carnosus clones containing either ORF1 or both ORFs together suggest that ORF1 and ORF2 represent the dehydrosqualene synthase gene (crtM) and the dehydrosqualene desaturase gene (crtN), respectively. The results furthermore suggest that the biosynthesis of 4,4'-diaponeurosporene starts with the condensation of two molecules of farnesyl diphosphate by dehydrosqualene synthase (CrtM); it is shown that the reaction product of this enzyme is dehydrosqualene and not squalene. Dehydrosqualene (4,4'-diapophytoene) is successively dehydrogenated by a desaturase (CrtN) to form the yellow main intermediate 4,4'-diaponeurosporene.

Amino Acid Sequence↗
PubMed2006

Cultivation of methanogens from shallow marine sediments at Hydrate Ridge, Oregon.

Little is known about the methanogenic degradation of acetate, the fate of molecular hydrogen and formate or the ability of methanogens to grow and produce methane in cold, anoxic marine sediments. The microbes that produce methane were examined in permanently cold, anoxic marine sediments at Hydrate Ridge (44 degrees 35' N, 125 degrees 10' W, depth 800 m). Sediment samples (15 to 35 cm deep) were collected from areas of active methane ebullition or areas where methane hydrates occurred. The samples were diluted into enrichment medium with formate, acetate or trimethylamine as catabolic substrate. After 2 years of incubation at 4 degrees C to 15 degrees C, enrichment cultures produced methane. PCR amplification and sequencing of the rRNA genes from the highest dilutions with growth suggested that each enrichment culture contained a single strain of methanogen. The level of sequence similarity (91 to 98%) to previously characterized prokaryotes suggested that these methanogens belonged to novel genera or species within the orders Methanomicrobiales and Methanosarcinales. Analysis of the 16S rRNA gene libraries from DNA extracted directly from the sediment samples revealed phylotypes that were either distantly related to cultivated methanogens or possible anaerobic methane oxidizers related to the ANME-1 and ANME-2 groups of the Archaea. However, no methanogenic sequences were detected, suggesting that methanogens represented only a small proportion of the archaeal community.

Carbon Dioxide↗
PubMed2000

MR imaging features of Nipah encephalitis.

OBJECTIVE: The newly discovered Nipah virus causes an acute febrile encephalitic illness in humans that is associated with a high mortality. The purpose of this study is to describe the MR imaging findings of Nipah encephalitis. MATERIALS AND METHODS: MR imaging of the brain was performed in 31 patients with Nipah encephalitis divided into three groups. The first group (14 patients) underwent MR imaging during the acute phase of the illness and the second group (10 patients) during the later phase of the acute illness. The third group consisted of six patients who underwent MR imaging because they experienced neurologic relapse and one patient who had late-onset encephalitis. Spin-echo T1- and T2-weighted sequences and T2-weighted fluid attenuated inversion recovery (FLAIR) sequences were performed. Contrast-enhanced MR imaging was performed in four patients. RESULTS: The FLAIR sequences revealed abnormalities in all patients studied. MR imaging findings in both the acute and later phases of encephalitis were similar; the main feature of both phases was the presence of discrete high-signal-intensity lesions, measuring 2-7 mm, disseminated throughout the brain, mainly in the subcortical and deep white matter of the cerebral hemispheres. Neither mass effect nor cerebral edema was seen. There was no correlation with the focal neurologic signs, depth of coma, and outcome of the patients. The lesions were attributed to widespread microinfarctions from underlying vasculitis of cerebral small vessels. Features found on MR imaging in relapsed and late-onset encephalitis differed from the features in acute encephalitis in that confluent cortical involvement was the prominent finding in the former, as opposed to discrete focal lesions in the subcortical and deep white matter in the latter. CONCLUSION: MR imaging is a sensitive and specific diagnostic tool for evaluating Nipah encephalitis.

Adolescent↗
PubMed1999

General properties and phylogenetic utilities of nuclear ribosomal DNA and mitochondrial DNA commonly used in molecular systematics.

To choose one or more appropriate molecular markers or gene regions for resolving a particular systematic question among the organisms at a certain categorical level is still a very difficult process. The primary goal of this review, therefore, is to provide a theoretical information in choosing one or more molecular markers or gene regions by illustrating general properties and phylogenetic utilities of nuclear ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA) that have been most commonly used for phylogenetic researches. The highly conserved molecular markers and/or gene regions are useful for investigating phylogenetic relationships at higher categorical levels (deep branches of evolutionary history). On the other hand, the hypervariable molecular markers and/or gene regions are useful for elucidating phylogenetic relationships at lower categorical levels (recently diverged branches). In summary, different selective forces have led to the evolution of various molecular markers or gene regions with varying degrees of sequence conservation. Thus, appropriate molecular markers or gene regions should be chosen with even greater caution to deduce true phylogenetic relationships over a broad taxonomic spectrum.

Animals↗
PubMedDate not supplied

The Sturge-Weber syndrome: comparison of MR and CT characteristics.

Four patients with Sturge-Weber syndrome were evaluated with CT and MR. MR demonstrated the characteristic features of the disease: cerebral atrophy (four patients), ipsilateral bone and sinus hypertrophy (three), ocular findings (one), intracranial calcification (four), prominent deep venous system (three), and enlarged choroid plexus (two). CT demonstrated the following: cerebral atrophy (four), ipsilateral bone and sinus hypertrophy (three), calcification (four), gyral enhancement (two), prominent deep venous system (two), and enlarged choroid plexuses (three). The features of Sturge-Weber syndrome were visualized equally well with MR and CT with the exception of intracranial calcification. Conventional spin-echo MR revealed fewer calcifications, and those visualized appeared smaller than with CT. Gradient-echo acquisition sequences were more effective in the detection of intracranial calcification.

Adolescent↗
PubMed1997

Ultrasound contrast agents. Examples of blood pool agents.

PURPOSE: The concept of contrast agents has been extended to ultrasonography (US) almost 30 years ago. Due to technical limitations, the development of US contrast agents (USCA) was slow until the last decade. The ideal USCA should be nontoxic, i.v. injectable, capable to cross the pulmonary capillary bed after a peripheral injection, and be stable enough to achieve enhancement for the total duration of the examination. It should provide not only Doppler but also B-mode enhancement, at a reasonable cost. The efficacy of the most advanced USCA has been reviewed. RESULTS AND CONCLUSION: Doppler examinations improved in cases of deep or small vessels, vessels with low or slow flow, or vessels studied with a bad insonation angle. USCA also enhanced detection of flow within normal and abnormal vessels, including tumor and stenotic vessels. Ischemic areas were better delineated. Specific settings and software developed by US equipment manufacturers and US sequences (such as second harmonic imaging or transient imaging) prefigured the necessary adaptation of US units to the new potentials of USCA. Second harmonic properties will improve detection of smaller vessels including neovascularization associated with tumors. Targeting possibilities will increase the efficacy of USCA, and allow specific delivery of active drugs such as anticoagulants or cytotoxic compounds. New generations of USCA appear very promising, and are becoming part of the US future.

Contrast Media↗
PubMed2025

CNV-Finder: Streamlining Copy Number Variation Discovery.

Copy Number Variations (CNVs) play pivotal roles in the etiology of complex diseases and are variable across diverse populations. Understanding the association between CNVs and disease susceptibility is significant in disease genetics research and often requires analysis of large sample sizes. One of the most cost-effective and scalable methods for detecting CNVs is based on normalized signal intensity values, such as Log R Ratio (LRR) and B Allele Frequency (BAF), from Illumina genotyping arrays. In this study, we present CNV-Finder, a novel pipeline integrating deep learning techniques on array data, specifically a Long Short-Term Memory (LSTM) network, to expedite the large-scale identification of CNVs within predefined genomic regions. This facilitates efficient prioritization of samples for time-consuming or costly subsequent analyses such as Multiplex Ligation-dependent Probe Amplification (MLPA), short-read, and long-read whole genome sequencing. We incorporate four genes to establish our methods-Parkin (PRKN), Leucine Rich Repeat And Ig Domain Containing 2 (LINGO2), Microtubule Associated Protein Tau (MAPT), and alpha-Synuclein (SNCA)-which may be relevant to neurological diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), Progressive Supranuclear Palsy (PSP), or related disorders such as essential tremor (ET). By training our models on expert-annotated samples and validating them across diverse cohorts, including those from the Global Parkinson's Genetics Program (GP2) and additional dementia-specific databases, we demonstrate the efficacy of CNV-Finder in accurately detecting deletions and duplications. Our pipeline outputs app-compatible files for visualization within CNV-Finder's interactive web application. This interface enables researchers to review predictions and filter displayed samples by model prediction values, LRR range, and variant count in order to explore or confirm results. Our pipeline integrates this human feedback to enhance model performance and reduce false positive rates. Through a series of comprehensive analyses and validations using visual inspection, MLPA, short-read, and long-read sequencing data, we demonstrate the robustness and adaptability of CNV-Finder in identifying CNVs with regions of varied size, probe density, and noise. Our findings highlight the significance of contextual understanding and human expertise in enhancing the precision of CNV identification, particularly in complex genomic regions like 17q21.31. The CNV-Finder pipeline is a scalable, publicly available resource for the scientific community, available on GitHub (https://github.com/GP2code/CNV-Finder; DOI 10.5281/zenodo.14182563). CNV-Finder not only expedites accurate candidate identification but also significantly reduces the manual workload for researchers, enabling future targeted validation and downstream analyses in regions or phenotypes of interest.

Copy Number Variation (CNV)↗
PubMed1991

Differentiating and mature neurons express the acidic fibroblast growth factor gene during chick neural development.

We have previously isolated and characterized acidic fibroblast growth factor (aFGF) from the embryonic chick brain. To analyze the expression of the gene encoding this growth factor a cDNA clone was isolated. The predicted amino acid sequence was found to be highly conserved (90%) between human and chick. Using single-stranded DNA probes, aFGF gene expression was detectable at day 3.5 in the embryonic chick brain. The mRNA level of the 1.7 kb transcript increased during embryonic development and reached the highest level in the adult brain. In situ hybridization results confirmed these developmental changes and revealed a localized expression in neurons. In the adult, Purkinje cells, deep cerebellar and brainstem neurons showed a high level of aFGF mRNA. In the embryonic brain, localized expression in neurons was detectable from day 6 onward. aFGF mRNA was also present in neurons of the peripheral nervous system. In dorsal root ganglia, aFGF was found to be expressed after embryonic day 6. Cells of blood vessels and the ependyma did not express detectable amounts of aFGF mRNA. These results suggest that aFGF may have a function as a differentiation or maintenance factor for postmitotic neurons or as a growth or differentiation factor for other cells in the nervous system mainly in later stages of development.

Amino Acid Sequence↗
PubMed2005

Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages.

BACKGROUND: Analysis of human complete mitochondrial DNA sequences has largely contributed to resolve phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this macrohaplogroup to precisely characterize and unravel the intricate phylogeny of the lineages and to establish the antiquity of M lineages in India. RESULTS: The phylogenetic tree constructed from sequencing information of twenty-four whole mtDNA genome revealed novel substitutions in the previously defined M2a and M6 lineages. The most striking feature of this phylogenetic tree is the recognition of two new lineages, M30 and M31, distinguished by transitions at 12007 and 5319, respectively. M30 comprises of M18 and identifies a potential new sub-lineage possessing substitution at 16223 and 16300. It further branches into M30a sub-lineage, defined by 15431 and 195A substitution. The age of M30 lineage was estimated at 33,042 YBP, indicating a more recent expansion time than M2 (49,686 YBP). The M31 branch encompasses the M6 lineage along with the previously defined M3 and M4 lineages. Contradictory to earlier reports, the M5 lineage does not always include a 12477 substitution, and is more appropriately defined by a transversion at 10986A. The phylogenetic tree also identifies a potential new lineage in the M* branch with HVSI sequence as 16223,16325. Substitutions in M25 were in concordance with previous reports. CONCLUSION: This study describes five new basal mutations and recognizes two new lineages, M30 and M31 that substantially contribute to the present understanding of macrohaplogroup M. These two newly erected lineages include the previously independent lineages M18 and M6 as sub-lineages within them, respectively, suggesting that most mt DNA genomes might arise as limited offshoots of M trunk. Furthermore, this study supports the non existence of lineages such as M3 and M4 that are solely defined on the basis of fast mutating control region motifs and hence, establishes the importance of coding region markers for an accurate understanding of the phylogeny. The deep roots of M phylogeny clearly establish the antiquity of Indian lineages, especially M2, as compared to Ethiopian M1 lineage and hence, support an Asian origin of M majorhaplogroup.

Amino Acid Motifs↗
PubMed2005

Analysis of mRNA in hemophilia A patients with undetectable mutations reveals normal splicing in the factor VIII gene.

BACKGROUND: haemophilia A (HA) is characterized by partial or total deficiency of factor VIII (FVIII) protein activity. It is caused by a broad spectrum of mutations in the FVIII gene. Despite tremendous improvements in mutation screening methods, in about 2% of HA patients no DNA change could be found, even after sequencing the whole coding part of the FVIII gene including the flanking splice sites, as well as the promotor and the 3' UTR regions. OBJECTIVES, PATIENTS AND METHODS: In the present study we performed a detailed RNA analysis of three groups of patients. The first included control patients with known splicing defects, the second included two patients with already identified nucleotide changes close to splicing sites, that could potentially alter the normal splicing process, and a third group of 11 unrelated patients whose genomic DNA have already been screened for mutations by DHPLC and direct sequencing with no mutation being identified. RESULTS: Both candidate splice site mutations were shown to result in either skipping or alternative splicing of at least one exon, therefore these DNA changes must be considered as causal for the patients' HA phenotype. In contrast, no abnormalities on the RNA level were observed in any of 11 unrelated patients without mutations in the FVIII gene. CONCLUSIONS: These findings exclude mutations that could be located deep in the introns and affecting either normal splicing or lead to mechanisms causing some unknown rearrangements of the FVIII gene. In fact, our results point to the presence of still unknown factor(s) causing HA, which might be either allelic or in the close proximity of the FVIII gene or non-allelic associated with other genetic loci that are involved in the processing of the FVIII protein.

DNA Mutational Analysis↗
PubMed1980

Quantitative assay of electromyograms during mastication in domestic cats (Felis catus).

Mastication has been studied by cinematography with synchronized electromyography (computer quantified and analyzed), while unanesthetized, freely feeding cats (Felis catus) were reducing equivalent-sized chunks of raw and cookded beef and cooked chicken. Cats reduce food on one side at a time, and their chewing cycles show horizontal and anteroposterior deflections. Food objects are shifted from side to side by lateral jerks of the head and movements of the tongue. During the opening phase, the lower jaw is rotated relatively straight downward, and the digastric muscles are active in bilateral symmetry. Near the end of opening, the head jerks upward, both zygomaticomandibulares start to fire, and opening acceleration of the mandible decreases. Closing starts with horizontal displacement of the mandibular canines toward the working side, accompanied by asymmetrical activities from the working side deep temporalis and the balancing side medial pterygoid, as well as a downward jerk of the head. As closing proceeds the mandibular canines remain near the working side and the working side zygomaticomandibularis and deep masseter are very active. Near the end of closing, the mandibular canine on the working side moves toward the midline, and adductors, digastrics, and lateral pterygoids of both sides are active. The adductors of the working side are generally more active than those of the balancing side. During a reduction sequence, the number and shape of the masticatory cycles, as well as movements of the head, during a reduction sequence are affected significantly by food type. As reduction proceeds, the duration of bite and the muscular activity (as characterized by number and amplitude of spikes) change significantly among muscles of the working and balancing sides. The adductors of the working side are generally most active when cats chew raw beef, less for cooked beef, and least for cooked chicken. In general, the adductor activity reflect food consistency, whereas that of the digastrics and lateral pterygoids reflects more the vertical and lateral displacements of the mandible. Statistical analysis documents that the methods of electrode insertion and test give repeatable results for particular sites in different animals. Thus, it should be possible to compare these results with those produced while other mammals are masticating.

Animals↗
PubMed1975

Cognitive processing and linguistic reference in autistic children.

Mutism or echolalia and failure to analyze sentences for their deep structures are characteristics of the language behavior of autistic children. The experimental literature indicates that cognitive processes which underlie the construction of a lexicon or the learning of ordering rules may be disturbed in these children. The inability to coordinate visual and aural stimulation inhibits lexical development, while difficulties in sequencing and use of inappropriate sequencing codes inhibits the growth of a productive grammar. It is suggested that remedial programs which include training in these processes may prove beneficial, and that substitute modes of information processing which the autistic child uses may be exploited to teach language forms.

Association Learning↗
PubMed1983

The simultaneous extraction of high-molecular-weight DNA and of RNA from solid tumors.

A novel method for the isolation of both macromolecular DNA and RNA from solid tissues based upon the disruption by vibration of deep-frozen material in a mechanical device termed Mikro-dismembrator, is described. This technique reveals a yield of, on the average, 1 to 3 mg of either DNA or RNA per gram of tissue. The quality of the purified nucleic acids permits the detailed analysis of integrated tumor virus DNA sequences and their mRNA transcripts. Furthermore, the efficient isolation of papilloma virions from keratinized wart tissue is facilitated by the application of the Mikro-dismembrator.

Animals↗
PubMed1994

Aggrecan in bovine tendon.

Large proteoglycans were purified by ion-exchange chromatography, gel filtration and CsCl gradient centrifugation from the compressed and tensional regions of adult bovine deep flexor tendon. Tryptic peptide maps of proteoglycan from the compressed region were very similar to maps of aggrecan from bovine articular cartilage, with evidence for the presence of all fifteen previously identified markers from the G1, G2 and G3 domains. The presence of aggrecan in these samples was confirmed by sequencing the G1 peptide YPIHTPR. The equivalent maps for large proteoglycan from tensional tendon were also consistent with the presence of aggrecan, and this was confirmed by sequencing three marker peptides from each of the G2 and G3 domains. However, G1 marker peptides were conspicuously absent from tensional samples. Northern blots for aggrecan mRNA showed high levels in cells from compressed tendon and articular cartilage. Extended exposure revealed a lower level of hybridization to RNA from tensional tendon as well. The results confirm that aggrecan, which is similar in core protein structure to articular cartilage aggrecan, is the predominant chondroitin sulfate-bearing large proteoglycan of compressed tendon. The results also indicate that aggrecan fragments lacking the G1 domain can account for the small amounts of chondroitin sulfate-bearing large proteoglycan in tensional regions of adult tendon.

Aggrecans↗
PubMed2006

Resolving the root of the avian mitogenomic tree by breaking up long branches.

Incomplete taxon sampling has been a major problem in resolving the early divergences in birds. Five new mitochondrial genomes are reported here (brush-turkey, lyrebird, suboscine flycatcher, turkey vulture, and a gull) and three break up long branches that tended to attract the distant reptilian outgroup. These long branches were to galliforms, and to oscine and suboscine passeriformes. Breaking these long branches leaves the root, as inferred by maximum likelihood and Bayesian phylogenetic analyses, between paleognaths and neognaths. This means that morphological, nuclear, and mitochondrial data are now in agreement on the position of the root of the avian tree and we can, move on to other questions. An overview is then given of the deepest divisions in the mitogenomic tree inferred from complete mitochondrial genomes. The strict monophyly of both the galloanseres and the passerines is strongly supported, leaving the deep six-way split within Neoaves as the next major question for which resolution is still lacking. Incomplete taxon sampling was also a problem for Neoaves, and although some resolution is now available there are still problems because current phylogenetic methods still fail to account for real features of DNA sequence evolution.

Animals↗
PubMed2001

Deep hypothermic circulatory arrest: II. Changes in electroencephalogram and evoked potentials during rewarming.

BACKGROUND: Electrophysiologic studies during rewarming after deep hypothermic circulatory arrest probe the state of the brain during this critical period and may provide insight into the neurological effects of circulatory arrest and the neurologic outcome. METHODS: Electroencephalogram (EEG) and evoked potentials were monitored during rewarming in 109 patients undergoing aortic surgery with hypothermic circulatory arrest. RESULTS: The sequence of neurophysiologic events during rewarming did not mirror the events during cooling. The evoked potentials recovered first followed by EEG burst-suppression and then continuous EEG. The time to recovery of the evoked potentials N20-P22 complex was significantly correlated with the time of circulatory arrest even in patients without postoperative neurologic deficits (r = 0.37, (p = 0.002). The nasopharyngeal temperatures at which continuous EEG activity and the N20-P22 complex returned were strongly correlated (r = 0.44, p = 0.0002; r = 0.41, p = 0.00003) with postoperative neurologic impairment. Specifically, the relative risk for postoperative neurologic impairment increased by a factor of 1.56 (95% CI 1.1 to 2.2) for every degree increase in temperature at which the EEG first became continuous. CONCLUSIONS: No trend toward shortened recovery times or improved neurologic outcome was noted with lower temperatures at circulatory arrest, indicating that the process of cooling to electrocerebral silence produced a relatively uniform degree of cerebral protection, independent of the actual nasopharyngeal temperature.

Aged↗
PubMed2003

NMR structure of Citrobacter freundii AmpD, comparison with bacteriophage T7 lysozyme and homology with PGRP domains.

AmpD is a bacterial amidase involved in the recycling of cell-wall fragments in Gram-negative bacteria. Inactivation of AmpD leads to derepression of beta-lactamase expression, presenting a major pathway for the acquisition of constitutive antibiotic resistance. Here, we report the NMR structure of AmpD from Citrobacter freundii (PDB accession code 1J3G). A deep substrate-binding pocket explains the observed specificity for low molecular mass substrates. The fold is related to that of bacteriophage T7 lysozyme. Both proteins bind zinc at a conserved site and require zinc for amidase activity, although the enzymatic mechanism seems to differ in detail. The structure-based sequence alignment identifies conserved features that are also conserved in the eukaryotic peptidoglycan recognition protein (PGRP) domains, including the zinc-coordination site in several of them. PGRP domains thus belong to the same fold family and, where zinc-binding residues are conserved, may have amidase activity. This hypothesis is supported by the observation that human serum N-acetylmuramyl-L-alanine amidase seems to be identical with a soluble form of human PGRP-L.

Amino Acid Sequence↗