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The discoidin domain family revisited : new members from prokaryotes and a homology-based fold prediction

Baumgartner, Stefan LU ; Hofmann, Kay ; Chiquet-Ehrismann, Ruth and Bucher, P (1998) In Protein Science 7(7). p.31-1626
Abstract

Members of the discoidin (DS) domain family, which includes the C1 and C2 repeats of blood coagulation factors V and VIII, occur in a great variety of eukaryotic proteins, most of which have been implicated in cell-adhesion or developmental processes. So far, no three-dimensional structure of a known example of this extracellular module has been determined, limiting the usefulness of identifying a new sequence as member of this family. Here, we present results of a recent search of the protein sequence database for new DS domains using generalized profiles, a sensitive multiple alignment-based search technique. Several previously unrecognized DS domains could be identified by this method, including the first examples from prokaryotic... (More)

Members of the discoidin (DS) domain family, which includes the C1 and C2 repeats of blood coagulation factors V and VIII, occur in a great variety of eukaryotic proteins, most of which have been implicated in cell-adhesion or developmental processes. So far, no three-dimensional structure of a known example of this extracellular module has been determined, limiting the usefulness of identifying a new sequence as member of this family. Here, we present results of a recent search of the protein sequence database for new DS domains using generalized profiles, a sensitive multiple alignment-based search technique. Several previously unrecognized DS domains could be identified by this method, including the first examples from prokaryotic species. More importantly, we present statistical, structural, and functional evidence that the D1 domain of galactose oxidase whose three-dimensional structure has been determined at 1.7 A resolution, is a distant member of this family. Taken together, these findings significantly expand the concept of the DS domain, by extending its taxonomic range and by implying a fold prediction for all its members. The proposed alignment with the galactose oxidase sequence makes it possible to construct homology-based three-dimensional models for the most interesting examples, as illustrated by an accompanying paper on the C1 and C2 domains of factor V.

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author
organization
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type
Contribution to journal
publication status
published
subject
keywords
Amino Acid Sequence, Bacterial Proteins/chemistry, Databases, Factual, Discoidins, Evolution, Molecular, Fungal Proteins/chemistry, Galactose Oxidase/chemistry, Lectins, Molecular Sequence Data, Protein Folding, Protein Structure, Tertiary, Protozoan Proteins, Sequence Alignment, Sequence Homology, Amino Acid
in
Protein Science
volume
7
issue
7
pages
31 - 1626
publisher
The Protein Society
external identifiers
  • scopus:0031826798
  • pmid:9684896
ISSN
0961-8368
DOI
10.1002/pro.5560070717
language
English
LU publication?
yes
id
803b1edd-c889-4a18-b2bd-7ddb15fc452e
date added to LUP
2019-05-21 14:21:45
date last changed
2019-12-03 02:10:04
@article{803b1edd-c889-4a18-b2bd-7ddb15fc452e,
  abstract     = {<p>Members of the discoidin (DS) domain family, which includes the C1 and C2 repeats of blood coagulation factors V and VIII, occur in a great variety of eukaryotic proteins, most of which have been implicated in cell-adhesion or developmental processes. So far, no three-dimensional structure of a known example of this extracellular module has been determined, limiting the usefulness of identifying a new sequence as member of this family. Here, we present results of a recent search of the protein sequence database for new DS domains using generalized profiles, a sensitive multiple alignment-based search technique. Several previously unrecognized DS domains could be identified by this method, including the first examples from prokaryotic species. More importantly, we present statistical, structural, and functional evidence that the D1 domain of galactose oxidase whose three-dimensional structure has been determined at 1.7 A resolution, is a distant member of this family. Taken together, these findings significantly expand the concept of the DS domain, by extending its taxonomic range and by implying a fold prediction for all its members. The proposed alignment with the galactose oxidase sequence makes it possible to construct homology-based three-dimensional models for the most interesting examples, as illustrated by an accompanying paper on the C1 and C2 domains of factor V.</p>},
  author       = {Baumgartner, Stefan and Hofmann, Kay and Chiquet-Ehrismann, Ruth and Bucher, P},
  issn         = {0961-8368},
  language     = {eng},
  number       = {7},
  pages        = {31--1626},
  publisher    = {The Protein Society},
  series       = {Protein Science},
  title        = {The discoidin domain family revisited : new members from prokaryotes and a homology-based fold prediction},
  url          = {http://dx.doi.org/10.1002/pro.5560070717},
  doi          = {10.1002/pro.5560070717},
  volume       = {7},
  year         = {1998},
}