HOMEODOMAIN family


General information Numeration assumed

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 151POU 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 c151 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 p159 - 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:


© M.Djumagulov, A.Alexeevski, A.Karyagina, S.Spirin

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