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An updated structural classification of substrate-binding proteins.

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Scheepers, Giel H., Lycklama a Nijeholt, Jelger A., Poolman, Bert·2016·FEBS Letters

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Abstract

Substrate-binding proteins (SBPs) play an important role in solute uptake and signal transduction. In 2010, Berntsson et al. classified the 114 organism-specific SBP structures available at that time and defined six protein clusters, based on their structural similarity. Since then, the number of unique SBP structures has increased almost fivefold, whereas the number of protein entries in the Protein Data Bank (PDB) nearly doubled. On the basis of the much larger dataset, we now subclassify the SBPs within the original clusters. Moreover, we propose a 7th cluster based on a small group of SBPs with structural features significantly different from those observed in the other proteins.

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PHYLIP-Phylogeny inference package (Version 3.2)
Felsenstein, J. (1989) · Cladistics · Cited by 17,682
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
Letunić, I., & Bork, P. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw290 · Cited by 5,023
ABC Transporters: From Microorganisms to Man
Higgins, C. F. (1992) · Annual Review of Cell Biology · doi:10.1146/annurev.cb.08.110192.000435 · Cited by 3,985
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
Krissinel, E., & Henrick, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904026460 · Cited by 3,788
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Rees, D. C., Johnson, E., & Lewinson, O. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2646 · Cited by 1,454
Mechanistic diversity in ATP-binding cassette (ABC) transporters.
Locher, K. P. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3216 · Cited by 804
Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria
Tam, R., & Saier, M. H. (1993) · Microbiological Reviews · doi:10.1128/mr.57.2.320-346.1993 · Cited by 732
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O’Hara, P. J., Sheppard, P. O., Thøgersen, H., Venezia, D., Haldeman, B. A., McGrane, V., Houamed, K. M., Thomsen, C., Gilbert, T., & Mulvihill, E. R. (1993) · Neuron · doi:10.1016/0896-6273(93)90269-w · Cited by 710
Mechanism of glutamate receptor desensitization
Sun, Y., Olson, R., Horning, M. S., Armstrong, N., Mayer, M. L., & Gouaux, E. (2002) · Nature · doi:10.1038/417245a · Cited by 662
FFAS03: a server for profile-profile sequence alignments
Jaroszewski, L., Rychlewski, L., Li, Z., Li, W., & Godzik, A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki418 · Cited by 590
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Schumacher, M. A., Choi, K. Y., Zalkin, H., & Brennan, R. G. (1994) · Science · doi:10.1126/science.7973627 · Cited by 371
Hinge-bending in L-arabinose-binding protein. The “Venus's-flytrap” model.
Mao, B., Pear, M. R., McCammon, J. A., & Quiocho, F. A. (1982) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)68161-5 · Cited by 268
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Fukami-Kobayashi, K., Tateno, Y., & Nishikawa, K. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2454 · Cited by 219
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Authors: Scheepers, G. H., Lycklama a Nijeholt, J. A., & Poolman, B.
Affiliations: University of Groningen (NL)
Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute Zernike Institute for Advanced Materials University of Groningen The Netherlands
Corresponding author: Poolman, Bert
ORCID: Scheepers, Giel H.
Poolman, Bert
Venue: FEBS Letters
Publisher: Wiley
Published: 2016-10-23
Volume: 590
Issue: 23
Pages: 4393-4401
ISSN: 0014-5793 (ISSN-L)
1873-3468
DOI: 10.1002/1873-3468.12445
OpenAlex: W2528162531
Cited by: 260
References: 47
Citations by year: 2026: 7 · 2025: 24 · 2024: 26 · 2023: 29 · 2022: 31 · 2021: 51 · 2020: 28 · 2019: 28 · 2018: 22 · 2017: 13 · 2016: 1
FWCI: 9.79
Type: journal article
Language: en
Open access: green
research.rug.nl
Licence: other-oa
onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations: FEBS Letters (publishedVersion)
PubMed (publishedVersion)
University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, other-oa)
Zenodo (CERN European Organization for Nuclear Research) (submittedVersion, other-oa)
University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
Funders: European Research Council (670578)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Health Sciences › Medicine › Oncology › Drug Transport and Resistance Mechanisms
Keywords: substrate-binding protein, structural classification, protein clusters, solute uptake, signal transduction, protein structure, Protein Data Bank
MeSH terms: Protein Conformation, alpha-Helical, Models, Molecular, Protein Binding, Proteins, Computational Biology, Databases, Protein

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An updated structural classification of substrate-binding proteins.

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