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Table 1 Structural features and role for DNA binding of different AmtR residues.

From: DNA binding by Corynebacterium glutamicum TetR-type transcription regulator AmtR

Sequence position

Effect on DNA binding

Location

Structural features

Equivalent residue in E. coli TetR

Glu23

o

NI

solvent exposed, only few interactions

Ser8

Glu30

++

NI

Glu30-Arg34 salt bridge

Glu15

Leu31

++

NI

buried

Leu16

Phe32

+++

NI

buried

Leu17

Thr33

o

NI

solvent exposed, only few interactions

Asn18

Gly36

o

NI

C-terminus of helix α1; only few interactions

Gly21

Thr40

++

NI

buried

Leu25

Thr42

o(+)

IF

backbone interactions with G3 phosphate group

Thr27

His43

+

IF

G3 ring

Arg28

Gly50

++

NI

tight turn

Gly35

Ile51

+++

NI

buried

Ile36

Arg52

+

IF

backbone contact with T-6 phosphate group

Glu37

Gln53

++

IF

side chain contacts with A4 ring

Gln38

Ala54

+

IF

weak non-polar interactions with the methyl group of T-6

Pro39

Ser55

++(+)

IF

side chain contacts with C-7

Thr40

Leu56

+++

NI

buried

Leu41

Tyr57

++(+)

IF

side chain contacts with A4 and T5

Tyr42

Tyr58

++(+)

IF

side chain interactions with DNA and with His59

Trp43

His59

+++

IF

side chain hydrogen bonds to protein and DNA

His44

Leu70

+++

NI

buried

Leu55

Leu71

++

NI

partially buried

Ala56

  1. The first and second column list the residues investigated and their experimentally determined effect on DNA binding. "o" indicates no effect, while increasing numbers of "+ signs qualitatively reflect the magnitude, by which DNA binding is decreased. Signs in parenthesis indicate minor differences between the two experimental methods used. The third and fourth column list the location of the residue in the structure as deduced from the AmtR-DNA model as well as key structural features that might be of relevance for DNA binding. "IF" and "NI" denote protein-DNA interface and non-interface residues, respectively. The last column shows the structurally equivalent residues in E. coli TetR.