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