Difference between revisions of "Reference APSES domains (yeast)"
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Latest revision as of 16:03, 26 September 2015
APSES domains in yeast
All APSES domains from APSES domain proteins in saccharomyces cerevisiae - annotated.
What is the APSES domain?
The APSES domain is a well-defined type of DNA-binding domain that is ubiquitous in fungi and unique in that kingdom. Structurally it is a member of the Winged Helix-Turn-Helix family. Recently it was found that it is homologous to the somewhat shorter, prokaryotic KilA-N domain; thus the APSES domain was retired from pFam and instances were merged into the KilA-N family. However InterPro has a KilA-N entry but still recognizes the APSES domain.
KilA-N domain boundaries in Mbp1 can be derived from the results of a CDD search with the ID 1BM8_A (the Mbp1 DNA binding domain crystal structure). The KilA-N superfamily domain alignment is returned.
- (pfam 04383): KilA-N domain; The amino-terminal module of the D6R/N1R proteins defines a novel, conserved DNA-binding domain (the KilA-N domain) that is found in a wide range of proteins of large bacterial and eukaryotic DNA viruses. The KilA-N domain family also includes the previously defined APSES domain. The KilA-N and APSES domains may also share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease.
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BM8A 16 IHSTGSIMKRKKDDWVNATHILKAANFAKaKRTRILEKEVLKETHEKVQ---------------GGFGKYQGTWVPLNIA 80
Cdd:pfam04383 3 YNDFEIIIRRDKDGYINATKLCKAAGETK-RFRNWLRLESTKELIEELSeennvdkseiiigrkGKNGRLQGTYVHPDLA 81
90
....*....|....
1BM8A 81 KQLA----EKFSVY 90
Cdd:pfam04383 82 LAIAswisPEFALK 95
Note that CDD and SMART are not consistent in how they apply pFam 04383 to the Mbp1 sequence. See annotation below.
The CDD KilA-N domain definition begins at position 16 of the 1BM8 sequence. But virtually all fungal APSES domains have a longer, structurally defined, conserved N-terminus. Blindly applying the KilA-N domain definition to these proteins would lose important information. For most purposes we will prefer the sequence spanned by the 1BM8_A structure. The sequence is given below, the KilA-N domain is coloured dark green. By this definition the APSES domain is 99 amino acids long and comprises residues 4 to 102 of the NP_010227 sequence.
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BM8A 1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGFGKYQGTWVPLNIA 80
90
....*....|....*....
1BM8A 81 KQLAEKFSVYDQLKPLFDF 99
- Yeast APSES domain sequence in FASTA format
>APSES_MBP1 Residues 4-102 of S. cerevisiae Mbp1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRI LEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF
- Synopsis of ranges
| Domain | Link | Length | Boundary | Range (Mbp1) | Range (1BM8) |
| KilA-N: pfam04383 (CDD) | CDD alignment | 72 | STGSI ... KFSVY | 21 - 93 | 18 - 90 |
| KilA-N: pfam04383 (SMART) | Smart main page | 79 | IHSTG ... YDQLK | 19 - 97 | 16 - 94 |
| KilA-N: SM01252 (SMART) | Smart main page | 84 | TGSIM ... DFTQT | 22 - 105 | 19 - 99... |
| APSES: Interpro IPR003163 | (Interpro) | 130 | QIYSA ... IRSAS | 3 - 133 | 1 - 99... |
| APSES (1BM8) | – | 99 | QIYSA ... PLFDF | 4 - 102 | 1 - 99 |
- To be newly created
Further reading and resources
