Table 3.

Sequence alignments between Cd-specific MerR mutants and MerR family members presented in the supplemental material

Mutation or region and mutationa	Mutant(s)	% of mutations in sequence alignment
		MerR (136)b	CadR/PbrR (92)	ZntR (64)	CueR/HmrR/PmtR/GolS (72)
E72A	B_DB4	7.4	32.6	0.0	5.4
E72D	B_DB17/26	5.9	0.0	6.3	16.2
L73I	B_DB10	0.0	0.0	0.0	0.0
L73F	B_DB17	0.0	0.0	1.6	4.1
L74W	B_DB4	0.0	0.0	0.0	0.0
R75W	B_DB4/10	0.0	0.0	0.0	0.0
L76I	B_DB17/27/29	2.2	0.0	96.9	0.0
L76V	B_DB10	12.5	1.1	0.0	0.0
Loop from residues D77 to H81c
D77E	B_D20/D_DB27	28.7
D77C	B_DB4	0.0
D77Y	B_DB10	0.0
D78E	B_DB17	5.9
G79Y	B_D20	0.0
T80S	B_DB4	5.1
T80N	B_DB26	0.0
T80A	B_DB29	10.3
H81G	All	1.5
E83V	All	0.7	0.0	1.6	1.4
E84G	All	1.5	13.0	0.0	0.0
A85H	All	0.0	0.0	0.0	0.0
S86D	All	0.0	0.0	0.0	0.0
S87A	All	14.7	48.9	31.3	45.9
K99R	C_DB21	14.0	95.7	20.3	55.4
M106L	C_DB21	16.9	100.0	1.6	16.2
V114T	B_D20, B_DB4/10/17/26/27/29	1.5	0.0	1.6	0.0
C115G	B_D20, B_DB4/10/17/26/27/29	3.7	2.2	0.0	1.4
C115Q	C_DB21	14.7	16.3	3.1	4.1
A116M	B_D20, B_DB4/10/17/26/27/29	0.0	0.0	0.0	0.0
A116P	C_DB21	0.0	0.0	0.0	0.0
Metal-binding loop from residues H118 to S125d
H118N	All B mutants	2.9
A119L	All B mutants	1.5
A119P	C_DB21	0.0
R120P	All B mutants	3.7
K121P	All	4.4
G122A	B_D20	4.4
G122R	B_DB4	2.2
N123K	B_DB10	2.2
N123Y	B_DB29	0.0
V124F	B_D20	0.7
V124Y	B_DB27	6.6
S125F	B_DB4	0.0
S125P	B_DB10	0.0
L128M	B_D20	3.7	0.0	0.0	0.0
L128F	B_DB4	0.0	0.0	0.0	0.0
I129V	B_DB4	2.9	22.8	0.0	0.0
A130R	B_DB17	0.0	7.6	0.0	4.1
A130E	B_DB27	21.3	5.4	71.9	18.9
S131T	B_D20	19.1	0.0	7.8	4.1

^aNumbering of the residues is based on that of MerR from Tn21. Highly conserved amino acids of MerR proteins are highlighted in boldface.

^bData in parentheses are the number of sequences used in the multiple-sequence alignment.

^cThe loop lengths of the MerR-like proteins were from 5 to 7 residues. CadR/PbrR, ZntR, and CueR/HmrR/PmtR/GolS were 2, 3, and 2 residues longer than MerR (Tn21), respectively. CadR/PbrR and CueR/HmrR/PmtR/GolS loop sequences contained conserved P and R, respectively. After the loop of CueR/HmrR/PmtR/GolS, there is an S instead of metal-binding C82. H and P residues were present in the loops of ZntR-like proteins.

^dThe motifs in the metal-binding loop were CysX₈Cys for MerR, CysX_5–9Cys for CadR/PbrR, CysX₉Cys (which has C and H residues involved in Zn binding) for ZntR, and CysXGlyX₄Asp/GluCys (in which there is a high degree of conservation of the D following the G) for CueR/HmrR/PmtR/GolS.