Table 1

Conserved sequence motifs found in EEP domains (labeled I through VI in Fig. 2) and the roles of specific amino acids in two EEP domains of known three-dimensional structure (APE1_Hs_1HD7, ExoIII_Ec_1AKO in Fig. 5–7).
REX1/REX2	APE1	EXO III

I. TWN	Asn forms a hydrogen bond to catalytic Asp in motif IV	Asn interacts with 5' phosphate group
II. QE	Glu coordinates Mg²⁺ion	Glu coordinates Mg²ion
III. HL	His is substituted by Tyr in APE1 but is the catalytic His in DNase I family	His is substituted by Tyr
IV. GDFN	Catalytic Asp deprotonates the water molecule; Asn forms a hydrogen bond to scissile phosphate	Asn forms a hydrogen bond to scissile phosphate
V. GRXD (X is S in REX1 and A in REX2)	Asp forms a hydrogen bond to His in motif VI	Asp forms a hydrogen bond to His in motif VI
VI. SDH	His forms a hydrogen bond to Asp in motif V and to scissile phosphate	Catalytic His deprotonates the water molecule and forms a hydrogen bond to Asp in motif V

Mian et al. BMC Bioinformatics 2006 7:305 doi:10.1186/1471-2105-7-305