Table 1.
Proteins in Saccharomyces cerevisiae genome predicted to have the thiol-disulfide oxidoreductase active site
| Functional motifb | Active site | ||||||||
| Sequence IDa | Thd/FFFc | CPd | Pr | PS | Bl | C | C/S | P | Database description |
| YLR043C (trx1) | X | X | X | X3e | Xc | 30 | 33 | 73 | Thioredoxin 1 |
| YGR209C (trx2) | X | X | X | X3c | Xe | 31 | 34 | 74 | Thioredoxin 2 |
| YCR083W (trx3) | X | X | X | X5c | Xf | 55 | 58 | 98 | Thioredoxin 3 |
| YDR513W (ttr1) | X | X | X | X4c | X | 61 | 64 | 110 | Glutaredoxin |
| YCL043C (PDI1) | X | X | — | X8c | Xc | 61 | 64 | 106 | PDI |
| X | X | X | X8c | Xc | 405 | 409 | 451 | ||
| YCL035C (YCD5) | X | X | X | X3c | X | 27 | 30 | 76 | Possible glutaredoxin |
| YCR288C (MPD1) | X | X | X | X10c | Xe | 59 | 62 | 105 | PDI related |
| YIL005W | X | X | — | X8f | Xc | 60 | 63 | 109 | Putative PDI |
| — | ? | X | 60 | 63 | 409 | ||||
| YLR364W | X | X | X2 | — | X2e | 25 | 28 | 74 | Hypothetical glutaredoxin-like |
| YBR014C | X | X | X | — | X | 108 | 111B | 156 | Possible glutaredoxin |
| YDL010W | X | X | — | — | X | 136 | 139B | 184 | Hypothetical protein |
| YDR518W (EUG1) | X | X | — | — | X | 62 | 65B | 107 | Possible disulfide isomerase |
| — | X | X | — | Xe | 405 | 408B | 453/459 | ||
| YOL088C (MPD2) | X | — | — | — | Xe | 56 | 59 | 96 | Possible disulfide isomerase |
| X | X | X | — | Xe | 56 | 59 | 106 | ||
| YER174C | X | X | X? | — | X3? | 171 | 174B | 213 | Hypothetical protein (now grx4) |
| YDR098C | X | X | X? | — | X4? | 211 | 214B | 253 | Possible thioredoxin (now grx3) |
| YPL059W | X | X | — | — | X2f | 60 | 63B | 105 | Possible glutared (now grx5) |
| YOR085W (OST3) | X | X | X2 | — | — | 73 | 76 | 133 | Oligosaccharyltransferase |
| YML019W (OST6) | X | X | — | — | — | 78 | 81 | 127 | Possible oligosaccharyltransferase |
| YDR286C | X | ? | — | — | X2e | 31 | 34 | 79 | Hypothetical protein |
| YNL155W | — | ? | X8e | — | — | 18 | 21 | ? | Hypothetical protein |
| X | ? | — | — | — | 31 | 34 | 164 | ||
| YDR133C | X | ? | — | — | — | 74 | 75 | 94 | Hypothetical protein |
| YDR199W | X | ? | — | — | — | 37 | 40 | 59 | Hypothetical protein |
| YOL024W | X | ? | — | — | — | 30 | 43B | 149 | Hypothetical protein |
| YKL102C | X | ? | — | — | — | 28 | 48 | 82 | Hypothetical protein |
| YLR245C (cdd1) | X | — | — | — | — | 59 | 61 | 112 | Cytidine deaminase |
| — | — | X5 | — | — | 96 | 99 | 112 | ||
| YLR246W (erf2) | X | — | — | — | — | 175 | 178 | 297 | Hypothetical protein |
| YHR002W | X | — | — | — | — | 198 | 201 | 299 | Possible mitochondrial carrier protein |
Question marks indicate that the sequence was identified as a thioredoxin by the Prints or Blocks motif libraries, but instead of the CXXC motif, an AXXC motif was found. For sequence YER174C the active site identified by the motif library was found to be A34 C36 P158, and for sequence YDR098C it was found to be A69 C72 P197. The same site, containing AXXC, was identified by both Prints and Blocks in each protein. The FFF identifies as alterative active site, containing the appropriate CXXC motif.
a Sequence number in the Saccharomyces genome sequence database.
b Search of each sequence found by Thread/FFF protocols against the local signature database (Prints (Pr; http://www.biochem.ucl.ac.uk/cgibin/attwood/SearchPrintsForm2.pl), Prosite (PS; http://expasy.hcuge.ch/sprot/acnpsit1.html), or BLocks (Bl; http://www.blocks.fhcrc.org/blocks_search.html). The number following the X indicates the rank of the sequence in the search.
c Top six alignments of S. cerevisiae operating from ORF to 1bed, 1ego, 1erv, 1fvk (chain A), 1kte, 1thx, 1tof, or 2trx (chain A), using threading (Jaroszewski et al. 1998), followed by scanning the sequence–sequence alignment for the active site residues specified by the FFF for the thiol-disulfide oxidoreductase activity of the glutaredoxin/thioredoxin family (Fetrow and Skolnick 1998).
d Conservation profile of homologous sequences demonstrates whether conservation of all three active site residues is >50%. For those sequences marked by a question mark, too few homologous sequences were found, so construction of a conservation profile was not possible.
e P motif not found.
f CXXC motif not found.
(FFF) fuzzy functional form; (CP) conservation profile; (Pr) Prints; (PS) Prosite; (Bl) Blocks; (C) cysteine; (C/S) cysteine or serine; (P) proline; (PDI) protein disulfide isomerase.