A gold standard set of mechanistically diverse enzyme superfamilies

Shoshana D Brown¹ , John A Gerlt² , Jennifer L Seffernick³ and Patricia C Babbitt⁴

¹Department of Biopharmaceutical Sciences, University of California, 1700 4th Street, San Francisco, San Francisco, CA 94143-2550, USA

²Department of Biochemistry, University of Illinois, Roger Adams Laboratory, 600 S Mathews Avenue, Urbana, IL 61801, USA

³Department of Biochemistry, Molecular Biology, and Biophysics, Biological Process Technology Institute, and Center for Microbial and Plant Genomics, University of Minnesota, St Paul, MN 55108, USA

⁴Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California, 1700 4th Street, San Francisco, San Francisco, CA 94143-2550, USA

author email corresponding author email

Genome Biology 2006, 7:R8doi:10.1186/gb-2006-7-1-r8


Published:	31 January 2006

Subject areas: Biochemistry and structural biology, Bioinformatics, Molecular biology

Additional files

Additional data file 1:

Superfamily and family assignments for each of the sequences and structures from this work, as well as the corresponding Pfam, SCOP, and SUPERFAMILY assignments. Pfam, SCOP, and SUPERFAMILY assignments are listed as names. ¹National Center for Biotechnology Information GI number. Additional data file 3 contains the fasta format sequences corresponding to each gi number. ²Protein Data Bank identifier. ³The gold and silver standard o -succinylbenzoate synthase (OSBS) families contain a more diverse set of enzymes than many other families listed in the table. All of the OSBS enzymes are believed to catalyze the same overall reaction via the same catalytic residues and there is no convincing evidence to suggest convergent evolution from within the superfamily, so we believe that these enzymes meet our definition of family. They appear, however, to utilize a different constellation of substrate binding residues, and certain subclusters within the family catalyze the promiscuous N-acyl amino acid racemase reaction in addition to the OSBS reaction. Because the sequences that comprise this family are highly divergent, it may pose special difficulties for automated clustering methods. Additional families that may be especially challenging include the extradiol dioxygenase families within the VOC superfamily, where a relatively high degree of sequence similarity and catalytic promiscuity make accurate clustering difficult. ⁴Evidence code for gold and silver standard family assignment [59]. ⁵ID number for the literature reference upon which gold/silver family assignment was based. When a sequence has been assigned to both a gold and silver standard family, this reference applies to both family classifications. When it has only been assigned to a silver standard family, this reference applies to the silver standard family classification. The full reference may be obtained by cross-referencing the ID number with Additional data file 4.

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Additional data file 2:

Superfamily and family assignments for each of the sequences and structures from this work, as well as the corresponding Pfam and SCOP assignments. Pfam and SCOP assignments are listed as accession numbers. This file is essentially identical to Additional data file 1, except that Pfam and SCOP assignments are listed as database accession numbers rather than names, and SUPERFAMILY assignments are not listed. ¹National Center for Biotechnology Information GI number. ²Protein Data Bank identifier. ³The gold and silver standard o -succinylbenzoate synthase (OSBS) families contain a more diverse set of enzymes than many other families listed in the table. All of the OSBS enzymes are believed to catalyze the same overall reaction via the same catalytic residues and there is no convincing evidence to suggest convergent evolution from within the superfamily, so we believe that these enzymes meet our definition of family. They appear, however, to utilize a different constellation of substrate binding residues, and certain subclusters within the family catalyze the promiscuous N-acyl amino acid racemase reaction in addition to the OSBS reaction. Because the sequences that comprise this family are highly divergent, it may pose special difficulties for automated clustering methods. Additional families that may be especially challenging include the extradiol dioxygenase families within the VOC superfamily, where a relatively high degree of sequence similarity and catalytic promiscuity make accurate clustering difficult. ⁴Evidence code for gold and silver standard family assignment [59]. ⁵ID number for the literature reference upon which gold/silver family assignment was based. When a sequence has been assigned to both a gold and silver standard family, this reference applies to both family classifications. When it has only been assigned to a silver standard family, this reference applies to the silver standard family classification. The full reference may be obtained by cross-referencing the ID number with Additional data file 4.

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Additional data file 3:

Fasta format sequences for gold standard superfamily proteins. Some protein sequences will differ from the sequence listed for the equivalent GI number at the National Center for Biotechnology Information, as they have been trimmed to remove portions of the sequence that are not part of the superfamily.

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Additional data file 4:

Literature references upon which gold and silver standard family assignments listed in Additional data file 1 and Additional data file 2 were made.

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Additional data file 5:

Gold and silver standard family assignments for each of the sequences in this work, including the corresponding evidence codes and literature references. ¹National Center for Biotechnology Information GI number. Additional data file 3 contains the fasta format sequences corresponding to each GI number. ²The gold and silver standard o -succinylbenzoate synthase (OSBS) families contain a more diverse set of enzymes than many other families listed in the table. All of the OSBS enzymes are believed to catalyze the same overall reaction via the same catalytic residues and there is no convincing evidence to suggest convergent evolution from within the superfamily, so we believe that these enzymes meet our definition of family. They appear, however, to utilize a different constellation of substrate binding residues, and certain subclusters within the family catalyze the promiscuous N-acyl amino acid racemase reaction in addition to the OSBS reaction. Because the sequences that comprise this family are highly divergent, it may pose special difficulties for automated clustering methods. Additional families that may be especially challenging include the extradiol dioxygenase families within the VOC superfamily, where a relatively high degree of sequence similarity and catalytic promiscuity make accurate clustering difficult. ³Evidence code for gold and silver standard family assignment [59]. ⁴ID number for the literature reference upon which gold/silver family assignment was based. This number corresponds to the reference ID number given in additional data files 1, 2, and 4. When a sequence has been assigned to both a gold and silver standard family, this reference applies to both family classifications. When it has only been assigned to a silver standard family, this reference applies to the silver standard family classification.

Format: XLS Size: 1.1MB Download file

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