PFRMAT AL 
TARGET T0056 
AUTHOR 7397-8542-2481 
METHOD ADDITIONAL INFORMATION 
METHOD From CASP target page: 6 alpha helices, residues: 30(I)-41(M),  
METHOD 47(W)-51(A),  
METHOD 64(H)-76(E), 84(I)-92(R), 103(A)-110(K),118(I)-134(M) 
METHOD 
METHOD Multiple sequence alignment of DnaB proteins suggested that the six 
METHOD helices of the N-terminal domain provide a scaffold for the invarient 
METHOD arginine at the C-terminal end of helix 6.  This arginine is proposed 
METHOD to be structurally equivalent to the "arginine finger" in RasGAP,  
METHOD RhoGAP, transducin alpha and the clamp-loader subunits.   
METHOD 
METHOD Because of the heterogeneity of structures serving as a scaffold for the 
METHOD "arginine finger", this insight was not considered a useful structural 
METHOD lead.  We searched for other potential templates using MAP without  
METHOD detecting convincing matches.  Eventually, we chose the C-terminal 
METHOD domain of the delta' subunit of the clamp-loader complex as a template, 
METHOD because it also contains six helices of similar length and amphipathic 
METHOD properties, and because its fold is a right-handed, up-and-down helical 
METHOD bundle, which is a frequently occurring fold.  
MODEL  1 
PARENT 1a5t 
I  30    E 214 
E  31    T 215 
A  32    L 216 
E  33    C 217 
Q  34    Q 218 
S  35    A 219 
V  36    L 220 
L  37    A 221 
G  38    Y 222 
G  39    S 223 
L  40    V 224 
M  41    P 225 
L  42    S 226 
D  43    D 228 
N  44    W 229 
E  45    Y 230 
R  46    S 231 
W  47    L 232 
D  48    L 233 
D  49    A 234 
V  50    A 235 
A  51    L 236 
H  64    A 241 
R  65    P 242 
H  66    A 243 
I  67    R 244 
F  68    L 245 
T  69    H 246 
E  70    W 247 
M  71    L 248 
A  72    A 249 
R  73    T 250 
L  74    L 251 
Q  75    L 252 
E  76    M 253 
S  77    D 254 
G  78    A 255 
S  79    L 256 
P  80    K 257 
I  84    P 271 
T  85    G 272 
L  86    L 273 
A  87    V 274 
E  88    A 275 
S  89    E 276 
L  90    L 277 
E  91    A 278 
R  92    N 279 
Q  93    H 280 
G  94    L 281 
A 103    G 291 
Y 104    D 292 
L 105    V 293 
A 106    C 294 
E 107    H 295 
L 108    I 296 
S 109    R 297 
K 110    E 298 
N 111    Q 299 
N 117    R 308 
I 118    E 309 
S 119    L 310 
A 120    L 311 
Y 121    I 312 
A 122    T 313 
D 123    D 314 
I 124    L 315 
V 125    L 316 
R 126    L 317 
E 127    R 318 
R 128    I 319 
A 129    E 320 
V 130    H 321 
V 131    Y 322 
R 132    L 323 
E 133    Q 324 
M 134    P 325 
I 135    G 326 
S 136    V 327 
TER 
END 
