
PFRMAT AL
TARGET T0100
AUTHOR 1020-4390-8741
REMARK Prediction team GERLOFF consists of the following
REMARK team members: Dietlind L. Gerloff (1),
REMARK Cairan Duffy (1), Zeti A. M. Hussein (1), 
REMARK 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 T0100 was by: DLG, CD, ZAMH, SWL.
METHOD 
METHOD This submission is a MANUAL THREADING ALIGNMENT for
METHOD Pectin Methylesterase from Erwinia chrysanthemi (T0100) using
METHOD a SINGLE-STRANDED RIGHT-HANDED BETA-HELIX as the parent fold,
METHOD as this was suggested by the majority of CAFASP2-submissions
METHOD 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 Amongst the available structures adopting a beta-helix fold,
METHOD we chose 1BHE (Polygalacturonase) and 1AIR (Pectate lyase) as our
METHOD two template structures for modelling based on their proximity in
METHOD the metabolic pathway (pectin/pectate degradation) and host
METHOD organism (Erwinia). 1BHE was chosen as the parent for submission
METHOD because of the higher sequence identity in pairwise alignments
METHOD with T0100 (approx. 20% vs. 17% for 1AIR) and better compatibility
METHOD with our prediction in most segments in places where the two
METHOD structures differ (with exception of the C-terminus; see below).
METHOD
METHOD The alignment proposed below was generated by matching clues 
METHOD from analysis of a multiple sequence alignment of the target
METHOD family (95 non-identical sequences & fragments) with the super-
METHOD imposed structures and multiple sequence alignments of their 
METHOD respective protein families. Homology searches were performed
METHOD by the PSI-BLAST server at PBIL (IBCP Lyon); alignments were 
METHOD generated by ClustalX and DARWIN and indel positions adjusted 
METHOD manually (several corrections were necessary).
METHOD   
METHOD The most important anchors for the threading alignment for this
METHOD target came from the distance constraints imposed by PUTATIVE
METHOD DISULFIDE BRIDGES in individual members of the T0100-family, and 
METHOD putative ACTIVE SITE RESIDUES (taking advantage of the approximately
METHOD equivalent active site location in bet-helix folds). 
METHOD The peculiarity that the Cys participating in the disulfide 
METHOD bridges are not conserved amongst
METHOD different subfamilies of Pectin methylesterases was noted by
METHOD Marcovic & Jornvall who determined the connectivity of the
METHOD tomato homolog (Protein Science 1:1288-1292 (1992). The same
METHOD holds true for the protein families of right-handed beta-helix
METHOD structures known today and indicate that the bridges are useful
METHOD but not mandatory for the maintenance of the fold. Probably due
METHOD to the topology, however, disulfide bridges are always formed
METHOD between Cys residues that are neighboring in the primary sequence;
METHOD in the known structures, they seem to be used either to stabilize
METHOD some of the extensive insertions in the core fold or to "clamp"
METHOD consecutive turns in the beta-helix. Given these restrictions and
METHOD the connectivities determined by the Jornvall group, the only way
METHOD to pair up the Cys residues in (nearly) all members was to place
METHOD them in equivalent locations in consecutive turns, away from the
METHOD active site grove. This is further consisten with the observation 
METHOD that some strand-strand junctions in the galacturonase and pectate
METHOD lyase folds, respectively, are less frequently used as insertion
METHOD sites (Jenkins et al., J.Struct.Biol. 122:236-246 (1998); Yoder &
METHOD Jurnak, FASEB J. 9:335-342 (1995); van Santen et al., J.Biol.Chem.
METHOD 274:30474-30480 (1999) and Chothia & Murzin, Structure 1:217-222 
METHOD (1993) were especially useful). Altogether, this analysis yielded
METHOD disulfide "clamps" for all central turns of the beta helix.
METHOD  
METHOD In addition, we identified absolutely and highly conserved, functional 
METHOD residues that are likely to be involved in the catalytic mechanism
METHOD and/or substrate binding at the active site. In accordance with the
METHOD anticipated anticipated general acid/base mechanism for ester hydro-
METHOD lysis and the location of the ester substituents' locations at one
METHOD side of the substrate, the putative active site residues in our
METHOD model are preferentially located in insertions on one side of the
METHOD substrate-binding grove, while they tend to occupy positions at
METHOD the bottom of the grove also in the galacturonase and pectate lyase
METHOD structures (where the pectin backbone is targeted by the enzyme).
METHOD 
METHOD Below, we submit fragments for the core parts of the beta-helix
METHOD fold only, i.e. we have omitted most of the insertions as we haven't
METHOD undertaken any detailed modeling studies for the loop segments. 
METHOD (One possibility to do so would be based on the geometrical constraints
METHOD imposed by a speculative catalytic mechanism.) As such, we are 
METHOD expecting that the fraction of superimposable C-alpha (and often
METHOD C-beta) atoms with the true structures will be indicative of the
METHOD validity of the assumptions and speculations used in the prediction
METHOD process - on the other hand, we might have missed out on fortuitous
METHOD superimposable atoms in the N- / C-terminal regions of the insertions. 
METHOD
METHOD Importantly, little attention was paid to the locations of the 
METHOD beta-strands in automated secondary structure predictions (e.g. PHD) 
METHOD as these are generally very difficult to predict accurately - 
METHOD instead, we tried to ALIGN PREDICTED SURFACE/INTERIOR POSITIONS 
METHOD as well as possible with the template structures given the 
METHOD long-range distance constraints described above. 
METHOD Surface/Interior positions were predicted as described,
METHOD e.g. in Benner et al., Chem.Rev. 97:2725-2843 (1997).
METHOD 
METHOD While it was generally possible to provide a satisfactory sequence-
METHOD structure alignment using 1BHE only as the designated parent structure,
METHOD this proved difficult in the last (C-terminal) turn of our T0100
METHOD model, where we would have preferred to either use 1AIR or the
METHOD C-terminal turn of 1BHE (which extends for two additional turns
METHOD compared with the other structures). However, in order to maintain
METHOD a single segment for evaluation, we list below the alignment with
METHOD the nearest positions in 1BHE. 
REMARK
MODEL  1
PARENT 1bhe
A  25  T  11
T  26  P  12
T  27  S  13
Y  28  S  14
N  29  C  15
A  30  T  16
V  31  T  17
V  32  L  18
S  33  K  19
K  34  A  20
S  35  D  21
G  39  S  23
K  40  T  24
T  41  A  25
F  42  T  26
K  43  S  27
T  44  T  28
I  45  I  29
A  46  Q  30
D  47  K  31
A  48  A  32
I  49  L  33
A  50  N  34
S  51  N  35
A  52  C  36
P  53  D  37
P  58  G  39
F  59  K  40
V  60  A  41
I  61  V  42
L  62  R  43
I  63  L  44
K  64  S  45
G  66  S  50
V  67  V  51
Y  68  F  52
N  69  L  53
E  70  S  54
R  71  P  56
L  72  L  57
T  73  S  58
I  74  L  59
T  75  P  60
R  76  S  61
N  78  G  62
L  79  V  63
H  80  S  64
L  81  L  65
K  82  L  66
G  83  I  67
E  84  D  68
S  85  K  69
R  86  G  70
N  87  V  71
G  88  T  72
A  89  L  73
V  90  R  74
I  91  A  75
S 112  F 102
S 113  I 103
T 114  T 104
I 115  A 105
T 116  V 106
S 118  S 107
A 119  T 108
K 120  T 109
D 121  N 110
F 122  S 111
S 123  G 112
A 124  I 113
Q 125  Y 114
S 126  G 115
L 127  G 117
T 128  T 118
I 129  I 119
R 130  D 120
N 131  G 121
T 152  P 151
Q 153  R 152
A 154  L 153
V 155  I 154
A 156  Q 155
L 157  I 156
Y 158  N 157
S 162  K 158
G 163  S 159
D 164  K 160
R 165  N 161
A 166  F 162
Y 167  T 163
F 168  L 164
K 169  Y 165
D 170  N 166
V 171  V 167
S 172  S 168
L 173  L 169
V 174  I 170
G 175  N 171
Y 176  S 172
Q 177  N 174
D 178  F 175
T 179  H 176
L 180  V 177
Y 181  V 178
V 182  F 179
S 183  S 180
G 184  D 181
G 185  G 182
R 186  D 183
S 187  G 184
F 188  F 185
F 189  T 186
S 190  A 187
D 191  W 188
C 192  K 189
I 194  T 190
S 195  T 191
G 196  I 192
V 198  T 201
D 199  D 202
F 200  G 203
I 201  I 204
F 202  D 205
G 203  P 206
G 205  K 210
T 206  N 211
A 207  I 212
L 208  T 213
F 209  I 214
N 210  A 215
N 211  Y 216
C 212  S 217
D 213  N 218
L 214  I 219
V 215  A 220
S 216  T 221
R 217  G 222
G 229  N 225
Y 230  V 226
L 231  A 227
T 232  I 228
A 233  K 229
P 234  A 230
S 235  Y 231
T 236  K 232
N 237  G 233
I 238  R 234
N 239  A 235
Q 240  E 236
K 241  T 237
Y 242  R 238
G 243  N 239
L 244  I 240
V 245  S 241
I 246  I 242
T 247  L 243
N 248  H 244
S 249  N 245
R 250  D 246
V 251  F 247
I 252  G 248
R 253  T 249
S 262  G 252
Y 263  M 253
G 264  S 254
L 265  I 255
G 266  G 256
R 267  S 257
P 268  E 258
W 269  T 259
H 270  M 260
A 285  G 261
I 286  V 262
G 287  Y 263
Q 288  N 264
T 289  V 265
V 290  T 266
F 291  V 267
L 292  D 268
N 293  D 269
T 294  L 270
S 295  K 271
M 296  M 272
F 325  G 274
F 326  T 275
E 327  T 276
Y 328  N 277
K 329  G 278
S 330  L 279
Y 331  R 280
G 332  I 281
A 333  K 282
G 334  S 283
A 335  D 284
K 339  K 285
D 340  S 286
R 341  A 287
R 342  A 288
Q 343  G 289
L 344  V 290
T 345  V 291
D 346  N 292
A 347  V 294
Q 348  R 295
A 349  Y 296
A 350  S 297
E 351  N 298
Y 352  V 299
T 353  V 300
Q 354  M 301
S 355  K 302
K 356  N 303
V 357  V 304
L 358  A 305
G 359  K 306
D 360  P 307
W 361  I 308
T 362  V 309
P 363  I 310
TER
END
 

