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Discovering structural motifs using a structural alphabet: application to magnesium-binding sites.

(2007) BMC Bioinformatics 8

PubMed: 17389049 | PubMedCentral: PMC1851716 | DOI: 10.1186/1471-2105-8-106

For example, 2 of the 3 proteins with the e(24–47)h(24)k motif (1SJC and 1TKK) possess Mg 2+ -binding domains pertaining to the enolase superfamily (CATH number 3.20.20.120), whereas the third... protein (2AKZ) has not yet been assigned a domain and therefore has no CATH number.

Although the n-acylamino acid racemase (1SJC) and gamma enolase (2AKZ) proteins do not share significant sequence homology (only 15.4% identity) and overall structure similarity (protein backbone rmsd = 17.5 Å), they possess similar Mg 2+ -binding site structures (backbone rmsd of the first-shell letters = 0.5 Å), as shown in Figure 5 .

(a) Cartoon diagram of the metal-binding domain in N-acylamino acid racemase (1SJC).

Table 2 1 st -shell structural motifs in Mg 2+ -proteins Motif a PDB code Mg 2+ -Ligands CATH number b Functional Group c EC code d e(24–47)h(24)k 1SJC D 189 , E 214 , D 239 3.20.20.120 Lyase e , Isomerase f - 1TKK D 191 , E 219 , D 244 3.20.20.120 Isomerase f - 2AKZ D 244 , E 292 , D 317 - Lyase e 4.2.1.11 f(1)h(109–349)b 1O08 D 1008 , D 1010 , D 1170 3.40.50.1000 Isomerase f 5.4.2.6 1U7P D 11 , D 13 , D 123 NYC Hydrolase g - 1WPG D 351 , T 353 , D 703 3.40.50.1000 Hydrolase g 3.6.3.8 2B82 D 44 , D 46 , D 167 3.40.50.1000 Hydrolase g 3.1.3.2 2C4N D 9 , D 11 , D 201 NYC Hydrolase g - f(2)h(126–158)m 1KA1 D 142 , D 145 , D 294 3.30.540.10 Hydrolase g 3.1.3.7 1NUY D 1118 , D 1121 , E 1280 3.30.540.10+ 3.40.190.80 Hydrolase g 3.1.3.11 2BJI E 1090 , D 1093 , D 1220 3.30.540.10+ 3.40.190.80 Hydrolase g 3.1.3.25 k(26–29)h(1)a 1ITZ D 168 , N 198 , I 200 3.40.50.970 Transferase h 2.2.1.1 1POX D 447 , N 474 , Q 476 3.40.50.970+ 3.40.50.1220 Oxidoreductase i 1.2.3.3 1UMD D 175 , N 204 , Y 206 3.40.50.970 Oxidoreductase i 1.2.4.4 1ZPD D 440 , N 467 , G 469 3.40.50.970 Lyase e 4.1.1.1 2C3M D 963 , T 991 , V 993 3.40.50.970 Oxidoreductase i 1.2.7.1 a The number in parentheses indicates the number of residues separating the letters corresponding to the Mg 2+ -bound residues.

(c) Superposition of the first-shell structural letters of 1SJC (blue) and 2AKZ (yellow).

Publication Year: 2007