
PFRMAT AL
TARGET T0101
AUTHOR 1020-4390-8741
REMARK Prediction team GERLOFF consists of the following
REMARK team members: Dietlind L. Gerloff (1),
REMARK Zeti A. M. Hussein (1), Melanie H. McCarthy-Troke (1), 
REMARK Cairan Duffy (1), Siu-wai Leung (2), Gina M. Cannarozzi (3).
REMARK (1): ICMB Biocomputing Research Unit & 
REMARK (2): Division of Informatics, University of Edinburgh;
REMARK (3): Computational Biochemistry Research Group, ETH Zurich
REMARK Contact email is Dietlind.Gerloff@ed.ac.uk
REMARK
REMARK Prediction for T0101 was by: DLG, ZAMH.
METHOD 
METHOD This submission is a MANUAL THREADING ALIGNMENT for a large
METHOD part of Pectate Lyase PelLfrom Erwinia chrysanthemi (T0101) using
METHOD a PECTATE LYASE A structure (SINGLE-STRANDED RIGHT-HANDED BETA-HELIX) 
METHOD as the parent fold. The fold is as suggested by the vast majority of 
METHOD CAFASP2-submissions for this target.
METHOD
METHOD WE SUBMIT THIS MANUAL THREADING ALIGNMENT WITH THE 
METHOD INTENTION TO ASSIST IN IMPROVING THE QUALITY OF AUTOMATED
METHOD THREADING ALIGNMENTS BY UNCOVERING WHICH OF THE CLUES COMMONLY
METHOD USED BY EXPERTS ALIGNING MANUALLY ARE MOST USEFUL AND COULD BE
METHOD EXPLORED SYSTEMATICALLY.
METHOD
METHOD Since PelL is reported to be a new class of Ca2+-dependent pectate
METHOD lyases we chose a pectate lyase structure as the parent fold. 1bn8
METHOD or 1air were considered as template structures for the threading;
METHOD this is the proposed sequence-structure alignment based on 1air.
METHOD We do not attribute much importance to our choice of parent structure -
METHOD rather, we hope to provide an acceptable threading alignment, which
METHOD is still problematic in many cases, particularly in the case of
METHOD repetitive structures (such as the turns of a beta helix).
METHOD 
METHOD For our alignment, we considered the set of homologs proposed by 
METHOD SAMT99 (kindly provided via the CAFASP-server prediction, and very
METHOD much acknowledged) which appears to be well-linked to ongoing
METHOD genome projects. Careful inspection of the sequences made us discard
METHOD a small number of sequences in the set. A ClustalX alignment was
METHOD used to help in this visual threading exercise; however due to the
METHOD repetitive features of the fold, the automated alignment had to
METHOD be adjusted in many places. Also, some alignment incertainties 
METHOD couldn't be resolved at all. 
METHOD 
METHOD In contrast to T0100, only extremely little help for the sequence-
METHOD structure alignment could be found obtained through speculative
METHOD disulfide bridges. Instead, we attempted to identify the coordinating
METHOD residues for the calcium ion. The identical conservation pattern of 
METHOD residues E167, N198, N249, and N255 made them possible candidates.
METHOD Most likely, E167, N198, and N249 would for the calcium binding
METHOD site, and N255 would play another key role in catalysis (possibly
METHOD that of a general base). Based on this hypothesis, we predict
METHOD that the folded structure of T0101 might look quite similar to
METHOD the currently known pectate lyases but the major loop excursions
METHOD from the beta helix core will be "shifted" two turns nearer to
METHOD the C-terminus. Incidentally, our hypothesis would place the
METHOD calcium ion at a similar location as it is found in co-crystal
METHOD structures (e.g. 1bn8). 
METHOD 
METHOD Prediction of the active site residues demanded that some of the
METHOD loops be "tightened", which is also important to assure there is
METHOD a cavity for the calcium. In order to achieve this, we had to 
METHOD cut out a segment of a core strand, between target# 196-199
METHOD because it might not superimpose with the corresponding segment
METHOD in 1air. Of course, there would have been alternative ways to
METHOD avoid the clashes, and we could also be mistaken in the exact
METHOD positions of the key residues.
METHOD 
METHOD For the remainder of the submitted alignment, we anchored in
METHOD positions that might be part of the characteristic Asn- and
METHOD Ser-ladders of pectate lyases. Overall, we regard this alignment
METHOD as somewhat sub-satisfactory because some large deletions and
METHOD insertions had to be made with respect to the template structure;
METHOD it is possible that we overlooked alternative possibilities due
METHOD to time pressure. It is even possible that a powerful pairwise 
METHOD sequence method would have produced a superior, or at least 
METHOD equivalent alignment between this target and its template structure,
METHOD as the automated fold recognition servers have all recognized the 
METHOD template fold so readily - we'll see.
METHOD 
REMARK
MODEL 1
PARENT 1air
S  56  S  20
F  57  K  21
N  58  T  22
A  59  A  23
M  61  T  24
S  62  S  25
F  63  M  26
S  64  Q  27
A  65  D  28
A  66  I  29
M  67  V  30
A  68  N  31
A  69  I  32
V  70  I  33
N  71  D  34
P  72  A  35
G  73  A  49
E  74  Y  50
L  75  P  51
I  76  L  52
L  77  V  53
L  78  I  54
K  79  T  55
P  80  Y  56
G  81  T  57
T  82  G  58
G 104  P  79
A 105  R  80
P 106  G  81
I 107  V  82
Y 108  E  83
V 109  I  84
A 110  K  85
A 111  E  86
A 112  F  87
N 113  T  88
A 117  G  90
V 118  I  91
F 119  T  92
D 120  I  93
F 121  I  94
S 122  G  95
F 123  A  96
G 134  G  98
F 135  S  99
Y 136  S 100
V 137  A 101
T 138  N 102
G 139  F 103
D 140  G 104
Y 141  I 105
W 142  W 106
Y 143  I 107
F 144  K 108
K 145  K 109
G 146  S 110
V 147  S 111
E 148  D 112
V 149  V 113
T 150  V 114
R 151  V 115
A 152  Q 116
G 153  N 117
Y 154  M 118
Q 155  R 119
G 156  I 120
A 157  G 121
N 176  G 130
T 177  D 131
G 178  M 132
L 179  I 133
E 180  R 134
I 181  V 135
N 182  D 136
N 183  D 137
G 184  S 138
N 188  N 140
T 189  V 141
V 190  W 142
I 191  V 143
N 192  D 144
S 193  H 145
D 194  N 146
A 195  E 147
Y 196  L 148
Y 199  V 169
D 200  D 170
P 201  I 171
K 202  K 172
K 203  G 173
F 211  A 174
G 212  S 175
P 213  N 176
K 214  T 177
Q 215  V 178
K 216  T 179
Q 217  V 180
G 218  S 181
G 220  Y 182
N 221  N 183
R 222  Y 184
F 223  I 185
V 224  H 186
G 225  G 187
C 226  V 188
R 227  K 189
A 228  K 190
W 229  V 191
E 230  G 192
N 231  L 193
S 232  D 194
D 233  G 195
D 234  S 196
G 235  S 197
F 236  S 198
D 237  S 199
L 238  D 200
F 239  T 201
D 240  G 202
S 241  R 203
P 242  N 204
Q 243  I 205
K 244  T 206
V 245  Y 207
V 246  H 208
I 247  H 209
E 248  N 210
N 249  Y 211
S 250  Y 212
W 251  N 213
A 252  D 214
F 253  V 215
R 254  N 216
N 255  A 217
G 256  R 218
F 272  P 220
K 273  L 221
L 274  Q 222
G 275  R 223
G 276  G 224
N 277  L 226
Q 278  V 227
A 279  H 228
V 280  A 229
G 281  Y 230
N 282  N 231
H 283  N 232
R 284  L 233
I 285  Y 234
T 286  T 235
R 287  N 236
S 288  I 237
V 289  T 238
A 290  S 240
F 291  G 241
G 292  L 242
N 293  N 243
V 294  V 244
S 295  R 245
G 305  N 247
G 306  G 248
V 307  Q 249
T 308  A 250
V 309  L 251
I 310  I 252
N 311  E 253
N 312  N 254
T 313  N 255
S 314  W 256
Y 315  F 257
K 316  E 258
N 317  K 259
G 318  A 260
I 319  I 261
N 320  N 262
Y 321  P 263
G 322  V 264
F 323  T 265
G 324  S 266
S 325  R 267
N 326  Y 268
V 327  D 269
Q 328  G 270
S 329  K 271
G 330  N 272
Q 331  F 273
K 332  G 274
H 333  T 275
Y 334  W 276
F 335  V 277
R 336  L 278
N 337  K 279
N 338  G 280
S 344  S 293
V 345  I 294
T 346  T 295
V 347  W 296
S 348  T 297
N 349  A 298
A 350  D 299
D 351  T 300
TER
END

