Computer-Based Annotation of Putative AraC/XylS-Family Transcription Factors of Known Structure but Unknown Function
Table 1
Known and putative TFs of the AraC/XylS family identified by a structural similarity search in the PDB.
Name (PDB code)
UniProt ID
DNA complex(a)
Technique (Res.)(b)
Species
Biological process
MarA (1bl0)
P0ACH5
Yes
X-ray (2.30 Å)
Escherichia coli
Multiple antibiotic resistance
MarA (1xs9)
P0ACH5
Yes
NMR
Escherichia coli
Multiple antibiotic resistance
Rob (1d5y)
P0ACI0
Yes
X-ray (2.70 Å)
Escherichia coli
Antibiotic resistance, organic solvent tolerance and heavy-metal resistance
Ada (1u8b)
P06134
Yes
X-ray (2.10 Å)
Escherichia coli
Repair of and response to alkylated DNA
Ada (1zgw)
P06134
Yes
NMR
Escherichia coli
Repair of and response to alkylated DNA
Ada (1wpk)
P06134
No
NMR
Escherichia coli
Repair of and response to alkylated DNA
GadX (3mkl)
B1X7X1
No
X-ray (2.15 Å)
Escherichia coli
Acid resistance
AraC (2k9s)
P0A9E0
No
NMR
Escherichia coli
Transport and catabolism of L-arabinose
TcpN or ToxT (3gbg)
A5F384
No
X-ray (1.90 Å)
Vibrio cholerae
Biosynthesis and assembly of the toxin-coregulated pilus
YesN (3lsg)
Q8RGT8
No
X-ray (2.05 Å)
Fusobacterium nucleatum
Possibly involved in plant cell wall degradation
Lin2118 protein (3oou)
Q92A04
No
X-ray (1.57 Å)
Listeria innocua
Unknown
3oio
Q7NTG7
No
X-ray (1.65 Å)
Chromobacterium violaceum
Unknown
3mn2
Q6NCA5
No
X-ray (1.80 Å)
Rhodopseudomonas palustris
Unknown
(a)Indicates whether the 3D protein structure was cocrystallized with DNA or not. (b)Numbers in parenthesis refer to the resolution of crystal structures.
