Reference APSES domains (yeast)

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

   

Further reading and resources

 

Multi FASTA file of all saccharomyces cerevisiae APSES domains.

Executing the PSI-BLAST search

The starting point of this list is a PSI-BLAST search with one known APSES domain sequence. This query sequence - the Mbp1 APSES domain - was defined as follows, based on Pfam profile 02292: APSES.

>Yeast Mbp1 APSES domain (AA 24..102 of NP_010227)
SIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGFGKY
QGTWVPLNIAKQLAEKFSVYDQLKPLFDF

Even though we are only interested in yeast genes, including other sequences into the PSI-BLAST search will allow us to identify distant homologues as well. A PSI-BLAST search was executed, searching in the refseq subset of GenPept and selecting an Organism restriction to use only Fungi (taxid: 4751). The default parameters for PSI-BLAST were used, except for using the BLOSUM45 matrix and an E-value threshold of 0.1, not 10.

The search converged after 6 iterations, i.e. in the 6th iteration PSI-BLAST found no additional new hits above the inclusion threshold E-value of 0.005. Clicking on the Taxonomy reports link lists all hits sorted by the species they originate from. Clicking on the Saccharomyces cerevisiae link identifies the yeast genes that were found:

 Saccharomyces cerevisiae S288c [ascomycetes] taxid 559292
ref|NP_010227.1| Mbp1p [Saccharomyces cerevisiae S288c]           126  1e-37
ref|NP_011036.1| Swi4p [Saccharomyces cerevisiae S288c]           103  9e-30
ref|NP_013729.1| Sok2p [Saccharomyces cerevisiae S288c]            98  9e-28
ref|NP_012881.1| Phd1p [Saccharomyces cerevisiae S288c]            94  2e-27
ref|NP_012165.1| Xbp1p [Saccharomyces cerevisiae S288c]            55  1e-12

One of these (Xbp1) is only a partial match with an alignment length of 55 amino acids. There is a somewhat complicated story here, therefore, for the purposes of the course I have removed Xbp1 from consideration as an APSES transcription factor. We will work from the four yeast gene families Mbp1, Swi4, Sok2, and Phd1.

Constructing the multi-FASTA file

A multi-FASTA file is the default input format for many MSA programs, it is simply a file that contains more than one FASTA formatted sequence.

The PSI-BLAST search has already defined the sequences from each source protein that are similar to the APSES search profile. We only need to extract them in a convenient way from the search results. NCBI offers options to format the result page: they are presented from a link at the top of the BLAST results page: " Reformat these Results": the principal options for the format are:

• Pairwise: the default
• Pairwise with identities: showing only differences to the query sequence
• query anchored with/without letters for identities: looks something like a multiple sequence alignment, hyphens for gaps, insertions relative to the query are displayed below the sequence
• flat-query anchored with/without letters for identities: This now looks like a multiple sequence alignment (in fact it is one - all sequences aligned to the profile).

I have selected the flat-query anchored with letters for identities option and restricted the output to saccharomyces cerevisiae sequences:

Query      1    SIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGFGKYQGTWVPLNIA  60
NP_010227  24   SIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGFGKYQGTWVPLNIA  83
NP_011036  60    VMRRTKDDWINITQVFKIAQFSKTKRTKILEKESNDMQHEKVQGGYGRFQGTWIPLDSA  118
NP_013729  436  SVVRRADNDMVNGTKLLNVTKMTRGRRDGILKAEKIRHV---VKIGSMHLKGVWIPFERA  492
NP_012881  208  SVVRRADNNMINGTKLLNVTKMTRGRRDGILRSEKVREV---VKIGSMHLKGVWIPFERA  264
NP_012165  343                                       NFTKRIRGGYIKIQGTWLPMEIS  365

Query      61   KQLAEKFS--VYD-QLKPLFDF  79
NP_010227  84   KQLAEKFS--VYD-QLKPLFDF  102
NP_011036  119  KFLVNKYE--IIDPVVNSILTF  138
NP_013729  493  LAIAQREK--IAD-YLYPLF    509
NP_012881  265  YILAQREQ--ILD-HLYPLF    281
NP_012165  366  RLLCLRFCFPIRY-FLVPIFG   385

I can then simply copy the alignment, remove hyphens and create FASTA headers to which I have manually added some useful information. The "Query" itself (being identical to the original Mbp1 protein) and the Xbp1 partial match are not included.

Yeast APSES domains

This is the final yeast APSES domain reference sequence set in multi-FASTA format.

>Mbp1_SACCE (79  ids)  NP_010227    (024..102)
SIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF
>Sok2_SACCE (74  ids)  NP_013729     (436..509)
SVVRRADNDMVNGTKLLNVTKMTRGRRDGILKAEKIRHVVKIGSMHLKGVWIPFERALAIAQREKIADYLYPLF
>Phd1_SACCE (74  ids)  NP_012881    (208..281)
SVVRRADNNMINGTKLLNVTKMTRGRRDGILRSEKVREVVKIGSMHLKGVWIPFERAYILAQREQILDHLYPLF
>Swi4_SACCE (79  ids)  NP_011036    (060..138)
VMRRTKDDWINITQVFKIAQFSKTKRTKILEKESNDMQHEKVQGGYGRFQGTWIPLDSAKFLVNKYEIIDPVVNSILTF