Linked Life Data

12012339

Source:http://linkedlifedata.com/resource/pubmed/id/12012339

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
1
pubmed:dateCreated
2002-5-23
pubmed:abstractText
Nitrogen regulatory (PII) proteins are signal transduction molecules involved in controlling nitrogen metabolism in prokaryots. PII proteins integrate the signals of intracellular nitrogen and carbon status into the control of enzymes involved in nitrogen assimilation. Using elaborate sequence similarity detection schemes, we show that five clusters of orthologs (COGs) and several small divergent protein groups belong to the PII superfamily and predict their structure to be a (betaalphabeta)(2) ferredoxin-like fold. Proteins from the newly emerged PII superfamily are present in all major phylogenetic lineages. The PII homologs are quite diverse, with below random (as low as 1%) pairwise sequence identities between some members of distant groups. Despite this sequence diversity, evidence suggests that the different subfamilies retain the PII trimeric structure important for ligand-binding site formation and maintain a conservation of conservations at residue positions important for PII function. Because most of the orthologous groups within the PII superfamily are composed entirely of hypothetical proteins, our remote homology-based structure prediction provides the only information about them. Analogous to structural genomics efforts, such prediction gives clues to the biological roles of these proteins and allows us to hypothesize about locations of functional sites on model structures or rationalize about available experimental information. For instance, conserved residues in one of the families map in close proximity to each other on PII structure, allowing for a possible metal-binding site in the proteins coded by the locus known to affect sensitivity to divalent metal ions. Presented analysis pushes the limits of sequence similarity searches and exemplifies one of the extreme cases of reliable sequence-based structure prediction. In conjunction with structural genomics efforts to shed light on protein function, our strategies make it possible to detect homology between highly diverse sequences and are aimed at understanding the most remote evolutionary connections in the protein world.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jul
pubmed:issn
1097-0134
pubmed:author
pubmed:copyrightInfo
Copyright 2002 Wiley-Liss, Inc.
pubmed:issnType
Electronic
pubmed:day
1
pubmed:volume
48
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
75-84
pubmed:dateRevised
2010-11-18
pubmed:meshHeading
pubmed-meshheading:12012339-Amino Acid Sequence, pubmed-meshheading:12012339-Animals, pubmed-meshheading:12012339-Bacterial Proteins, pubmed-meshheading:12012339-Binding Sites, pubmed-meshheading:12012339-DNA-Binding Proteins, pubmed-meshheading:12012339-Evolution, Molecular, pubmed-meshheading:12012339-Hydrophobic and Hydrophilic Interactions, pubmed-meshheading:12012339-Ligands, pubmed-meshheading:12012339-Metals, pubmed-meshheading:12012339-Models, Molecular, pubmed-meshheading:12012339-Molecular Sequence Data, pubmed-meshheading:12012339-Nitrogen, pubmed-meshheading:12012339-PII Nitrogen Regulatory Proteins, pubmed-meshheading:12012339-Protein Folding, pubmed-meshheading:12012339-Protein Structure, Secondary, pubmed-meshheading:12012339-Sensitivity and Specificity, pubmed-meshheading:12012339-Sequence Alignment, pubmed-meshheading:12012339-Sequence Analysis, Protein, pubmed-meshheading:12012339-Sequence Homology, Amino Acid, pubmed-meshheading:12012339-Trans-Activators, pubmed-meshheading:12012339-Transcription Factors
pubmed:year
2002
pubmed:articleTitle
Expanding the nitrogen regulatory protein superfamily: Homology detection at below random sequence identity.
pubmed:affiliation
Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
pubmed:publicationType
Journal Article