HOMEODOMAIN family

Numeration and designations assumed in this study

   For this study 36 PDB-entries containing coordinates of Homeodomains were used. Complete information about the studied structures, including the name of PDB-entry, the name of the chain representing Homeodomain, number of conserved ASN that bind to conserved adenine in DNA helix, other domains in PDB-entry, experimental method, resolution, presence of the DNA and water etc., is listed in the following table:

Information about the studied structures

PDB code	Chains	# of the 51th ASN in PDB file	Other domains	Experimental method	Resolution,Å	DNA	Water	Protein	UniProt code	Species
1AHD	p	51	-	NMR	-	Yes	No	Homeotic protein antennapedia	P02833	Drosophila melanogaster
1AKH	a	120	-	X-RAY	2.5	Yes	Yes	MATa1	P01366	Saccharomyces cerevisiae
	b	182						MATα2	Q6B2C0
1APL	c d	182 182	-	X-RAY	2.7	Yes	No	MATα2	Q6B2C0	Saccharomyces cerevisiae
1AU7	a b	151 151	POU domain	X-RAY	2.3	Yes	Yes	PIT-1	P10037	Rattus norvegicus
1B72	a	253	-	X-RAY	2.35	Yes	Yes	Hox-2I	P14653	Homo sapiens
	b	286						PBX1	P40424
1B8I	a	151	-	X-RAY	2.4	Yes	Yes	ultrabithorax	P83949	Drosophila melanogaster
	b	254						Dpbx	P40427
1CQT	a b	151 651	POU domain	X-RAY	3.2	Yes	No	Oct-1	P14859	Homo sapiens
1DU0	a b	51 151	-	X-RAY	2.0	Yes	Yes	Segmentation polarity homeobox protein engrailed	P02836	Drosophila melanogaster
1E3O	c	151	POU domain	X-RAY	1.9	Yes	Yes	Oct-1	P14859	Homo sapiens
1FJL	a b c	51 51 51	-	X-RAY	2.0	Yes	Yes	Segmentation protein paired	P06601	Drosophila melanogaster
1GT0	c	151	POU domain, HMG box	X-RAY	2.6	Yes	Yes	Oct-1	P14859	Mus musculus
1HDD	c d	51 51	-	X-RAY	2.8	Yes	No	Engrailed	P02836	Drosophila melanogaster
1HF0	a b	151 151	POU domain	X-RAY	2.7	Yes	Yes	Oct-1	P14859	Homo sapiens
1IG7	a	151	-	X-RAY	2.2	Yes	Yes	MSX-1	P13297	Mus musculus
1JGG	a b	151 351	-	X-RAY	2.0	Yes	Yes	Even-skipped	P06602	Drosophila melanogaster
1K61	a b c d	182 182 182* 182*	-	X-RAY	2.1	Yes	Yes	MATα2	P01367	Saccharomyces cerevisiae
1LE8	a	120	-	X-RAY	2.3	Yes	Yes	MATa1	P01366	Saccharomyces cerevisiae
	b	—						MATα2	Q6B2C0
1LFU	p	51	-	NMR	-	Yes	No	PBX1	P41778	Mus musculus
1MNM	c d	182 182	chain a - SRF-TF chain b - SRF-TF	X-ray	2.25	Yes	Yes	MATα2	Q6B2C0	Saccharomyces cerevisiae
1NK2	p	159	-	NMR	N/A	Yes	No	Vnd	P22808	Drosophila melanogaster
1NK3	p	151	-	NMR	N/A	Yes	No	Vnd	P22808	Drosophila melanogaster
1O4X	a	154	POU domain, HMG box	NMR	N/A	Yes	No	Oct-1	P14859	Homo sapiens
1OCT	c	151	POU domain	X-ray	3.00	Yes	No	Oct-1	P14859	Homo sapiens
1PUF	a	255	-	X-ray	1.90	Yes	Yes	Hox-A9	P09631	Homo sapiens
	b	286						PBX1	P40424
1YRN	a	120	-	X-ray	2.50	Yes	Yes	MATa1	P01366	Saccharomyces cerevisiae
	b	182						MATα2	Q6B2C0
1YZ8	p	51*	-	NMR	N/A	Yes	No	PITX2	Q99697	Homo sapiens
1ZQ3	p	52	-	NMR	N/A	Yes	No	PRD-4	Q9UAM0	Drosophila melanogaster
2D5V	a b	147 147	CUT CUT	X-ray	2.00	Yes	Yes	HNF-6	P70512	Rattus norvegicus
2H1K	a b	51 51	-	X-ray	2.42	Yes	Yes	PDX1	P70118	Mesocricetus auratus
2HDD	a b	51 51	-	X-ray	1.90	Yes	Yes	Engrailed	P02836	Drosophila melanogaster
2HOS	a b	51 51* +	-	X-ray	1.90	Yes	Yes	Engrailed	P02836	Drosophila melanogaster
2HOT	a b	51 51+	-	X-ray	2.19	Yes	Yes	Engrailed	P02836	Drosophila melanogaster
2R5Y	a	151	-	X-ray	2.60	Yes	Yes	Sex combs reduced	P09077	Drosophila melanogaster
	b	251+						Dpbx	P40427
2R5Z	a	151	-	X-ray	2.60	Yes	Yes	Sex combs reduced	P09077	Drosophila melanogaster
	b	251+						Dpbx	P40427
3HDD	a b	51 51	-	X-ray	2.20	Yes	Yes	Engrailed	P02836	Drosophila melanogaster
9ANT	a b	51 51	-	X-ray	2.40	Yes	Yes	Antennapedia	P02833	Drosophila melanogaster

* These ASN residues do not bind DNA
+ These ASN have inverted position
— This ASN was directly mutated to ALA

   Then multiple alignment of different proteins with the best resolution from these 36 structures was performed by means of SSM server. The protein sequences derived from PDB-files were aligned using GENEDOC. The picture of this alignment is as follows:

Download alignment in msf

   According to the gaps present in the alignment, all chains were renumbered so that after each gap the numeration begins from a new number. Thus, all aligned residues of different structures go under the same number and the gaps in the alignment do not put the numeration out. The residue corresponding to the number in the upper line is located under the last figure of the number. Thus, the residue 51 would be ASN, not GLN, which would be 50.
   The lower line called helices, according on SSM server alignment data, represents regions of the AA residues that form &alpha -helix conformation in all given PDB-entries.

   Nucleotide sequences of all homeodomain binding sites in every studied PDB-entry were also aligned using GENEDOC. Every aligned sequence is given name of PDB-entry and chain identifier of protein that contains homeodomain which binds with this nucleotide sequence. The alignment obtained reveals conserved nucleotide A in position 3 that binds with ASN-51. Nucleotides in positions 1-4 form so-called core, which is recognized by homeodomain and typically has -TAAT- sequence, although exceptions are very often.

* Homeodomain complex interacts with DNA from other asymmetrical unit, which means that part of nucleotide sequence is taken from there.
** In this homeodamain complex ASN-51 is mutated on ALA.

Download alignment in msf

Aligned nucleotide sequences were analyzed for similarities among them using MEME service. The obtained motif is shown below:

S&S main page  < Previous page