@inbook {16769, title = {CBMcarb-DB: interface of the three-dimensional landscape of carbohydrate-binding modules}, booktitle = {Carbohydrate Chemistry: Chemical and Biological Approaches Volume 46}, volume = {46}, year = {2024}, note = {n/a}, month = {2024/06/26}, publisher = {Royal Society of Chemistry}, organization = {Royal Society of Chemistry}, abstract = {

Carbohydrate-binding-modules (CBMs) are discrete auxiliary protein modules with a non-catalytic carbohydrate-binding function and that exhibit a great diversity of binding specificities. CBMcarb-DB is a curated database that classifies the three-dimensional structures of CBM{\textendash}carbohydrate complexes determined by single-crystal X-ray diffraction methods and solution NMR spectroscopy. We designed the database architecture and the navigation tools to query the database with the Protein Data Bank (PDB), UniProtKB, and GlyTouCan (universal glycan repository) identifiers. Special attention was devoted to describing the bound glycans using simple graphical representation and numerical format for cross-referencing to other glycosciences and functional data databases. CBMcarb-DB provides detailed information on CBMs and their bound oligosaccharides and features their interactions using several open-access applications. We also describe how the curated information provided by CBMcarb-DB can be integrated with AI algorithms of 3D structure prediction, facilitating structure{\textendash}function studies. Also in this chapter, we discuss the exciting convergence of CBMcarb-DB with the glycan array repository, which serves as a valuable resource for investigating the specific binding interactions between glycans and various biomolecular targets. The interaction of the two fields represents a significant milestone in glycosciences. CBMcarb-DB is freely available at https://cbmdb.glycopedia.eu/ and https://cbmcarb.webhost.fct.unl.pt.

}, isbn = {978-1-83767-217-2}, url = {https://doi.org/10.1039/BK9781837672844-00001}, author = {Ribeiro, D. O. and Bonnardel, F. and Palma, A. S. and Carvalho, A. L. M. and Perez, S.}, editor = {Pilar Rauter, Am{\'e}lia and Queneau, Yves and Palma, Angelina S{\'a}} } @article {ijms19041184, title = {The Crystal Structure of the R280K Mutant of Human p53 Explains the Loss of DNA Binding}, journal = {International Journal of Molecular Sciences}, volume = {19}, number = {4}, ARTICLE NUMBER = {1184}, year = {2018}, note = {n/a}, abstract = {

The p53 tumor suppressor is widely found to be mutated in human cancer. This protein is regarded as a molecular hub regulating different cell responses, namely cell death. Compelling data have demonstrated that the impairment of p53 activity correlates with tumor development and maintenance. For these reasons, the reactivation of p53 function is regarded as a promising strategy to halt cancer. In the present work, the recombinant mutant p53R280K DNA binding domain (DBD) was produced for the first time, and its crystal structure was determined in the absence of DNA to a resolution of 2.0 {\r A}. The solved structure contains four molecules in the asymmetric unit, four zinc(II) ions, and 336 water molecules. The structure was compared with the wild-type p53 DBD structure, isolated and in complex with DNA. These comparisons contributed to a deeper understanding of the mutant p53R280K structure, as well as the loss of DNA binding related to halted transcriptional activity. The structural information derived may also contribute to the rational design of mutant p53 reactivating molecules with potential application in cancer treatment.

}, issn = {1422-0067}, doi = {10.3390/ijms19041184}, url = {http://www.mdpi.com/1422-0067/19/4/1184}, author = {Gomes, Ana Sara and Trov{\~a}o, Filipa and Andrade Pinheiro, Benedita and Freire, Filipe and Gomes, Sara and Oliveira, Carla and Domingues, Luc{\'\i}lia and Rom{\~a}o, Maria Jo{\~a}o and Saraiva, Luc{\'\i}lia and Carvalho, Ana Lu{\'\i}sa} } @article {1799, title = {Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {24}, year = {2003}, note = {n/a}, pages = {13809-13814}, abstract = {n/a}, author = {Carvalho, AL and Dias, FMV and Prates, JAM and Nagy, T and Gilbert, HJ and Davies, GJ and Ferreira, LMA and Romao, MJ and Fontes, CMGA} } @article {1803, title = {Crystal structure of a prostate kallikrein isolated from stallion seminal plasma: A homologue of human PSA}, journal = {Journal of Molecular Biology}, volume = {322}, number = {2}, year = {2002}, note = {n/a}, pages = {325-337}, abstract = {n/a}, author = {Carvalho, AL and Sanz, L. and Barettino, D and Romero, A. and Calvete, JJ and Romao, MJ} } @article {1811, title = {Crystal structure of acidic seminal fluid protein (aSFP) at 1.9 angstrom resolution: a bovine polypeptide of the spermadhesin family}, journal = {Journal of Molecular Biology}, volume = {274}, number = {4}, year = {1997}, note = {

ISI Document Delivery No.: YP198 Times Cited: 33 Cited Reference Count: 32 Romao, MJ Kolln, I Dias, JM Carvalho, AL Romero, A Varela, PF Sanz, L Topfer-Petersen, E Calvete, JJ ACADEMIC PRESS LTD LONDON

}, pages = {650-660}, abstract = {

We report the three-dimensional crystal structure of acidic seminal fluid protein (aSFP), a 12.9 kDa poly-peptide of the spermadhesin family isolated from bovine seminal plasma, solved by the multiple isomorphous replacement method and refined with data to 1.9 Angstrom resolution with a final R-factor of 17.3\%. aSFP is built by a single CUB domain architecture, a 100 to 110 amino-acid-residue extracellular module found in 16 functionally diverse proteins. The structure of aSFP reveals that the CUB domain displays a beta-sandwich topology organised into two 5-stranded beta-sheets, each of which contain two parallel and four antiparallel strands. The structure of aSFP is almost identical to that of porcine spermadhesins PSP-I and PSP-II, which in turn show limited structural similarity with jellyroll topologies of certain virus capsid proteins. Essentially, topologically conserved residues in these proteins are those internal amino acids forming the hydrophobic core of the CUB and the jellyroll domains, suggesting their importance in maintaining the integrity of these protein folds, On the other hand, the structure of aSFP shows structural features that are unique to this protein and which may provide a structural ground for understanding the distinct biological properties of different members of the spermadhesin protein family. (C) 1997 Academic Press Limited.

}, keywords = {bovine seminal plasma protein acidic seminal fluid protein aSFP spermadhesins CUB domain PELLUCIDA BINDING CHARACTERISTICS BOAR SPERMADHESINS PLASMA OLIGOSACCHARIDE LOCALIZATION LOCATION}, author = {Romao, MJ and Kolln, I. and Dias, JM and Carvalho, AL and Romero, A. and Varela, P. F. and Sanz, L. and Topfer-Petersen, E. and Calvete, JJ} } @article {1812, title = {The crystal structures of two spermadhesins reveal the CUB domain fold}, journal = {Nature Structural Biology}, volume = {4}, number = {10}, year = {1997}, note = {

ISI Document Delivery No.: YA203 Times Cited: 108 Cited Reference Count: 32 Romero, A Romao, MJ Varela, PF Kolln, I Dias, JM Carvalho, AL Sanz, L TopferPetersen, E Calvete, JJ NATURE PUBLISHING CO NEW YORK

}, pages = {783-788}, abstract = {

Spermadhesins, 12,000-14,000 M-r mammalian proteins, include lectins involved in sperm-egg binding and display a single CUB domain architecture. We report the crystal structures of porcine seminal plasma PSP-I/PSP-II, a heterodimer of two glycosylated spermadhesins. and bovine aSFP at 2.4 Angstrom and 1.9 Angstrom resolution respectively.

}, keywords = {SEMINAL FLUID PROTEIN BOAR SPERMADHESINS PSP-II PLASMA HETERODIMER LOCATION CLONING RNA}, author = {Romero, A. and Romao, MJ and Varela, P. F. and Kolln, I. and Dias, JM and Carvalho, AL and Sanz, L. and TopferPetersen, E. and Calvete, JJ} } @article {1806, title = {Crystallization and preliminary x-ray diffraction studies of aSFP, a bovine seminal plasma protein with a single CUB domain architecture}, journal = {Protein Science}, volume = {6}, number = {3}, year = {1997}, note = {

ISI Document Delivery No.: WM740 Times Cited: 7 Cited Reference Count: 22 Dias, JM Carvalho, AL Kolln, I Calvete, JJ TopferPetersen, E Varela, PF Romero, A Urbanke, C Romao, MJ CAMBRIDGE UNIV PRESS NEW YORK

}, pages = {725-727}, abstract = {

{Bovine acidic seminal fluid protein (aSFP) is a 12.9 kDa polypeptide of the spermadhesin family built by a single CUB domain architecture. The CUB domain is an extracellular module present in 16 functionally diverse proteins. To determine the three-dimensional structure of aSFP, the protein was crystallized at 21 degrees C by vapor diffusion in hanging drops, using ammonium sulfate, pH 4.7, and polyethyleneglycol 4000 as precipitants, containing 10\% dioxane to avoid the formation of clustered crystals. Elongated prismatic crystals with maximal size of 0.6 x 0.3 x 0.2 mm(3) diffract to beyond 1.9 Angstrom resolution and belong to space group P2(1)2(1)2, with cell parameters a = 52.4 Angstrom

}, keywords = {acidic seminal fluid protein analytical ultracentrifugation aSFP bovine seminal plasma crystallization CUB domain spermadhesin protein family X-ray diffraction analysis FLUID PROTEIN BOAR SPERMADHESINS ZONA-PELLUCIDA LOCALIZATION AWN-1}, author = {Dias, JM and Carvalho, AL and Kolln, I. and Calvete, JJ and TopferPetersen, E. and Varela, P. F. and Romero, A. and Urbanke, C. and Romao, MJ} }