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Genome-based identification and analysis of collagen-related structural motifs in bacterial and viral proteins.

Rasmussen, Magnus LU ; Jacobsson, Micael and Björck, Lars LU (2003) In Journal of Biological Chemistry 278(34). p.32313-32316
Abstract
Collagens are extended trimeric proteins composed of the repetitive sequence glycine-X-Y. A (c) under bar ollagen- related (S) under bar tructural (m) under bar otif (CSM) containing glycine-X-Y repeats is also found in numerous proteins often referred to as collagen-like proteins. Little is known about CSMs in bacteria and viruses, but the occurrence of such motifs has recently been demonstrated. Moreover, bacterial CSMs form collagen-like trimers, even though these organisms cannot synthesize hydroxyproline, a critical residue for the stability of the collagen triple helix. Here we present 100 novel proteins of bacteria and viruses (including bacteriophages) containing CSMs identified by in silico analyses of genomic sequences. These... (More)
Collagens are extended trimeric proteins composed of the repetitive sequence glycine-X-Y. A (c) under bar ollagen- related (S) under bar tructural (m) under bar otif (CSM) containing glycine-X-Y repeats is also found in numerous proteins often referred to as collagen-like proteins. Little is known about CSMs in bacteria and viruses, but the occurrence of such motifs has recently been demonstrated. Moreover, bacterial CSMs form collagen-like trimers, even though these organisms cannot synthesize hydroxyproline, a critical residue for the stability of the collagen triple helix. Here we present 100 novel proteins of bacteria and viruses (including bacteriophages) containing CSMs identified by in silico analyses of genomic sequences. These CSMs differ significantly from human collagens in amino acid content and distribution; bacterial and viral CSMs have a lower proline content and a preference for proline in the X position of GXY triplets. Moreover, the CSMs identified contained more threonine than collagens, and in 17 of 53 bacterial CSMs threonine was the dominating amino acid in the Y position. Molecular modeling suggests that threonines in the Y position make direct hydrogen bonds to neighboring backbone carbonyls and thus substitute for hydroxyproline in the stabilization of the collagen-like triple-helix of bacterial CSMs. The majority of the remaining CSMs were either rich in proline or rich in charged residues. The bacterial proteins containing a CSM that could be functionally annotated were either surface structures or spore components, whereas the viral proteins generally could be annotated as structural components of the viral particle. The limited occurrence of CSMs in eubacteria and lower eukaryotes and the absence of CSMs in archaebacteria suggests that DNA encoding CSMs has been transferred horizontally, possibly from multicellular organisms to bacteria. (Less)
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author
organization
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Contribution to journal
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published
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in
Journal of Biological Chemistry
volume
278
issue
34
pages
32313 - 32316
publisher
ASBMB
external identifiers
  • wos:000184782100108
  • scopus:0042357053
ISSN
1083-351X
DOI
language
English
LU publication?
yes
id
f944839d-43d6-4c4b-a118-ca9d3a285951 (old id 116102)
alternative location
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12788919&dopt=Abstract
date added to LUP
2007-07-05 09:46:02
date last changed
2018-06-10 03:43:28
@article{f944839d-43d6-4c4b-a118-ca9d3a285951,
  abstract     = {Collagens are extended trimeric proteins composed of the repetitive sequence glycine-X-Y. A (c) under bar ollagen- related (S) under bar tructural (m) under bar otif (CSM) containing glycine-X-Y repeats is also found in numerous proteins often referred to as collagen-like proteins. Little is known about CSMs in bacteria and viruses, but the occurrence of such motifs has recently been demonstrated. Moreover, bacterial CSMs form collagen-like trimers, even though these organisms cannot synthesize hydroxyproline, a critical residue for the stability of the collagen triple helix. Here we present 100 novel proteins of bacteria and viruses (including bacteriophages) containing CSMs identified by in silico analyses of genomic sequences. These CSMs differ significantly from human collagens in amino acid content and distribution; bacterial and viral CSMs have a lower proline content and a preference for proline in the X position of GXY triplets. Moreover, the CSMs identified contained more threonine than collagens, and in 17 of 53 bacterial CSMs threonine was the dominating amino acid in the Y position. Molecular modeling suggests that threonines in the Y position make direct hydrogen bonds to neighboring backbone carbonyls and thus substitute for hydroxyproline in the stabilization of the collagen-like triple-helix of bacterial CSMs. The majority of the remaining CSMs were either rich in proline or rich in charged residues. The bacterial proteins containing a CSM that could be functionally annotated were either surface structures or spore components, whereas the viral proteins generally could be annotated as structural components of the viral particle. The limited occurrence of CSMs in eubacteria and lower eukaryotes and the absence of CSMs in archaebacteria suggests that DNA encoding CSMs has been transferred horizontally, possibly from multicellular organisms to bacteria.},
  author       = {Rasmussen, Magnus and Jacobsson, Micael and Björck, Lars},
  issn         = {1083-351X},
  language     = {eng},
  number       = {34},
  pages        = {32313--32316},
  publisher    = {ASBMB},
  series       = {Journal of Biological Chemistry},
  title        = {Genome-based identification and analysis of collagen-related structural motifs in bacterial and viral proteins.},
  url          = {http://dx.doi.org/},
  volume       = {278},
  year         = {2003},
}