ArticleProtein science : a publication of the Protein Society2004
Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold-type I, pyridoxal-5'-phosphate-dependent enzymes.
Article in Protein science : a publication of the Protein Society, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- Article
- Large scale analyses of genotype-phenotype relationships of glycine decarboxylase mutations and neurological disease severity.PLoS computational biology · 2020Article
- Biophysical characterization and molecular phylogeny of human KIN protein.European biophysics journal : EBJ · 2019Article
- Computational classification of MocR transcriptional regulators into subgroups as a support for experimental and functional characterization.Bioinformation · 2019Article
- Type I pyridoxal 5'-phosphate dependent enzymatic domains embedded within multimodular nonribosomal peptide synthetase and polyketide synthase assembly lines.BMC structural biology · 2013Article
- Structural mimicry between SLA/LP and Rickettsia surface antigens as a driver of autoimmune hepatitis: insights from an in silico study.Theoretical biology & medical modelling · 2013Article
- The structural biology of enzymes involved in natural product glycosylation.Natural product reports · 2012Review
- Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase.The EMBO journal · 2011Article
- Comprehensively surveying structure and function of RING domains from Drosophila melanogaster.PloS one · 2011Article
- Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences.BMC bioinformatics · 2009Article
- Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase.Biochemistry · 2008Article
- SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences.BMC bioinformatics · 2008Article
- Article
- Molecular architecture of DesV from Streptomyces venezuelae: a PLP-dependent transaminase involved in the biosynthesis of the unusual sugar desosamine.Protein science : a publication of the Protein Society · 2007Article
- Article
- Crystal structure of Homo sapiens kynureninase.Biochemistry · 2007Article
- Conversion of 5-aminolevulinate synthase into a more active enzyme by linking the two subunits: spectroscopic and kinetic properties.Protein science : a publication of the Protein Society · 2005Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The wealth of biological information provided by structural and genomic projects opens new prospects of understanding life and evolution at the molecular level. In this work, it is shown how computational approaches can be exploited to pinpoint protein structural features that remain invariant upon long evolutionary periods in the fold-type I, PLP-dependent enzymes. A nonredundant set of 23 superposed crystallographic structures belonging to this superfamily was built. Members of this family typically display high-structural conservation despite low-sequence identity. For each structure, a multiple-sequence alignment of orthologous sequences was obtained, and the 23 alignments were merged using the structural information to obtain a comprehensive multiple alignment of 921 sequences of fold-type I enzymes. The structurally conserved regions (SCRs), the evolutionarily conserved residues, and the conserved hydrophobic contacts (CHCs) were extracted from this data set, using both sequence and structural information. The results of this study identified a structural pattern of hydrophobic contacts shared by all of the superfamily members of fold-type I enzymes and involved in native interactions. This profile highlights the presence of a nucleus for this fold, in which residues participating in the most conserved native interactions exhibit preferential evolutionary conservation, that correlates significantly (r = 0.70) with the extent of mean hydrophobic contact value of their apolar fraction.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.