HTH3 family

Numeration and designations assumed in this study

   7 PDB entries containing coordinates of HTH3 domains were used in this study. These entries represent 4 proteins from two bacteriphages: phage lambda and phage 434. As 6 PDB entries contain 2 copies of HTH3 domain, they were divided into files with single copy of the domain, so that they could be superposed. Finally 13 structures of HTH3 domain were obtained and analyzed. All files contain coordinates of the DNA bound to protein and coordinates of molecules of water. All structures were obtained by means of x-ray diffraction. Information about the studied structures, including the name of PDB-entry, the name of the chain representing HTH3 domain, number of the corresponding model in structural alignment file, resolution, UniProt entry etc., is listed in the following table:

Information about the studied structures

PDB code	Chain	Model	PDB residues	Resolution	UniProt entry	Protein	Species
1lli	A	1	22 - 77	2,10	RPC1_LAMBD	Lambda C1 repressor	Bacteriophage lambda
1lli	B	4	22 - 77	2,10	RPC1_LAMBD	Lambda C1 repressor	Bacteriophage lambda
1lmb	3	5	22 - 77	1,80	RPC1_LAMBD	Lambda C1 repressor	Bacteriophage lambda
1lmb	4	6	22 - 77	1,80	RPC1_LAMBD	Lambda C1 repressor	Bacteriophage lambda
1per	L	2	7-60	2,50	RPC1_BP434	434 C1 repressor	Bacteriophage 434
1per	R	7	7-60	2,50	RPC1_BP434	434 C1 repressor	Bacteriophage 434
1rio	A	8	23 - 78	2,30	RPC1_LAMBD	Lambda C1 repressor	Bacteriophage lambda
1rio	B	9	23 - 78	2,30	RPC1_LAMBD	Lambda C1 repressor	Bacteriophage lambda
1rpe	L	10	7-60	2,50	RPC1_BP434	434 C1 repressor	Bacteriophage 434
1rpe	R	11	7-60	2,50	RPC1_BP434	434 C1 repressor	Bacteriophage 434
3cro	L	3	6-59	2,50	RCRO_BP434	434 cro	Bacteriophage 434
3cro	R	12	6-59	2,50	RCRO_BP434	434 cro	Bacteriophage 434
6cro	R	13	2-37	3,00	RCRO_LAMBD	Lambda cro	Bacteriophage lambda

   Both the sequence alignment of the studied HTH3 domains and the binding site DNA alignment were performed and are shown below:

Protein sequence alignment

Binding site sequence alignment

On these alignments sequence names are colored according to the protein they belong. On protein sequence alignment the lines after the 2Dstructur line represent the distributionsecond structure elements of corresponding domain, H stands for alpha-helix and S stands for beta-sheet. Line Aligned shows whether the respective residues are aligned on structural alignment, A stands for aligned residues, L stands for second structure elements which are similarly arranged in space, but actually cannot be aligned.    As it can be seen in the picture, only 2-nd and 3-rd alpha-helices and three loops are conserved in sequence, meanwhile they are also aligned in structure. To provide possibility to correctly address aligned residues of all domain examples, they were renumbered. Thus the first aligned residue was given number 101, not aligned residues after region of simiarity were renumbered from 201, while the initial numbering of not aligned residues before the region of similarity was kept.    The numbering of the DNA strands of the HTH3 binding site was also altered. The nucleotide contacting to Gln 115 (adenine in all DNA strand) was given number 801, the complementary nucleotide of the revers strand being given number 901.