Dataset Information

The FSSP database of structurally aligned protein fold families.

ABSTRACT: FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank (PDB). The database currently contains an extended structural family for each of 330 representative protein chains. Each data set contains structural alignments of one search structure with all other structurally significantly similar proteins in the representative set (remote homologs, < 30% sequence identity), as well as all structures in the Protein Data Bank with 70-30% sequence identity relative to the search structure (medium homologs). Very close homologs (above 70% sequence identity) are excluded as they rarely have marked structural differences. The alignments of remote homologs are the result of pairwise all-against-all structural comparisons in the set of 330 representative protein chains. All such comparisons are based purely on the 3D co-ordinates of the proteins and are derived by automatic (objective) structure comparison programs. The significance of structural similarity is estimated based on statistical criteria. The FSSP database is available electronically from the EMBL file server and by anonymous ftp (file transfer protocol).

SUBMITTER: Holm L

PROVIDER: S-EPMC308329 | biostudies-other | 1994 Sep

REPOSITORIES: biostudies-other

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The FSSP database of structurally aligned protein fold families.

Holm L L Sander C C

Nucleic acids research 19940901 17

FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank (PDB). The database currently contains an extended structural family for each of 330 representative protein chains. Each data set contains structural alignments of one search structure with all other structurally significantly similar proteins in the representative set (remote homologs, < 30% sequence identity), as well as all structures in the Protein Data Bank with 70-30 ...[more]

PMID: 7937067

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Project description:BACKGROUND: The prediction of biochemical function from the 3D structure of a protein has proved to be much more difficult than was originally foreseen. A reliable method to test the likelihood of putative annotations and to predict function from structure would add tremendous value to structural genomics data. We report on a new method, Structurally Aligned Local Sites of Activity (SALSA), for the prediction of biochemical function based on a local structural match at the predicted catalytic or binding site. RESULTS: Implementation of the SALSA method is described. For the structural genomics protein PY01515 (PDB ID 2aqw) from Plasmodium yoelii, it is shown that the putative annotation, Orotidine 5'-monophosphate decarboxylase (OMPDC), is most likely correct. SALSA analysis of YP_001304206.1 (PDB ID 3h3l), a putative sugar hydrolase from Parabacteroides distasonis, shows that its active site does not bear close resemblance to any previously characterized member of its superfamily, the Concanavalin A-like lectins/glucanases. It is noted that three residues in the active site of the thermophilic beta-1,4-xylanase from Nonomuraea flexuosa (PDB ID 1m4w), Y78, E87, and E176, overlap with POOL-predicted residues of similar type, Y168, D153, and E232, in YP_001304206.1. The substrate recognition regions of the two proteins are rather different, suggesting that YP_001304206.1 is a new functional type within the superfamily. A structural genomics protein from Mycobacterium avium (PDB ID 3q1t) has been reported to be an enoyl-CoA hydratase (ECH), but SALSA analysis shows a poor match between the predicted residues for the SG protein and those of known ECHs. A better local structural match is obtained with Anabaena beta-diketone hydrolase (ABDH), a known ?-diketone hydrolase from Cyanobacterium anabaena (PDB ID 2j5s). This suggests that the reported ECH function of the SG protein is incorrect and that it is more likely a ?-diketone hydrolase. CONCLUSIONS: A local site match provides a more compelling function prediction than that obtainable from a simple 3D structure match. The present method can confirm putative annotations, identify misannotation, and in some cases suggest a more probable annotation.

Dataset Information

The FSSP database of structurally aligned protein fold families.

Publications

The FSSP database of structurally aligned protein fold families.

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