
PFRMAT AL
TARGET T0087
AUTHOR 1020-4390-8741
REMARK Prediction team GERLOFF consists of the following
REMARK team members: Dietlind L. Gerloff (1),
REMARK Melanie H. McCarthy-Troke (1),
REMARK Zeti A. M. Hussein (1), Cairan Duffy (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 T0087 was by: DLG, ZAMH.
METHOD
METHOD This submission consists of MANUAL FOLD RECOGNITION PREDICTION(s) 
METHOD for and THREADING ALIGNMENTS for two predicted domains in T0087.
METHOD The predictions use the fold of the THIAMINE-BINDING DOMAIN as
METHOD the parent fold (the fold of the so-called PP- and Pyr-domains
METHOD of TPP-using enzymes). The specific template structure, trans-
METHOD ketolase (1trk) was chosen because of the possible resemblance
METHOD of the C-terminal domain with the template; any other fold in 
METHOD the PP-binding family would have considered adequate.
METHOD 
METHOD The essential clue and prediction strategy used for the first domain
METHOD lies in the predicted location of the Mn(2+) which is relevant for
METHOD catalytic function, and the compatibility with the predicted fold
METHOD and threading alignment with the anticipated, approximate
METHOD composition and geometry of a polyphosphate hydrolase site. 
METHOD Specifically, we postulate that target residues D13, D15, D76,
METHOD D97, H98, H99, and D150 play a role in metal binding, or catalysis.
METHOD These positions are conserved in a medium-wide alignment containing
METHOD the homologs retrieved by SAMT99 (CAFASP-server) and the public
METHOD access to these sequences is very much acknowledged.
METHOD Interestingly, the location of these residues in the predicted
METHOD alpha/beta secondary structure narrows down the number of possible
METHOD beta sheet topologies by requiring the key players to be at the
METHOD ends of adjacent strands (strands 1, 3, and 4, primarily). This
METHOD fact RULES OUT A ROSSMANN FOLD.
METHOD 
METHOD No functional clues were available for the C-terminal domain but
METHOD the expected solvent accessibility of the predicted strands etc.
METHOD suggests the C-terminal domain of transketolase might be a possible
METHOD template (predicted only for reasons of possible common ancestral
METHOD linkage between the target and 1trk).
METHOD 
METHOD WE ARE VERY CONFIDENT ABOUT THE PREDICTION FOR THE FIRST DOMAIN.
METHOD 
REMARK Model 1 and 2 are based on the PP- and PYR-domains of 1trk, respec-
REMARK tively, for the N-terminal domain, and the C-terminal domain of 1trk
REMARK for the C-terminus. The chain is terminated between them as we have
REMARK no reliable grounds for assuming that the inter-domain orientation
REMARK should be conserved. Model 3 is an unterminated form of Model 2 in
REMARK order to have the two domains assessed together in case the domain
REMARK orientation were the same as in 1trk after all.
MODEL  2
PARENT 1trk_A
M   1  Q 372
S   2  L 373
K   3  P 374
I   4  E 375
L   5  L 376
V   6  I 377
F   7  G 378
G   8  G 379
H   9  S 380
Q  10  A 381
N  11  D 382
P  12  L 383
D  13  T 384
G  31  G 409
V  32  R 410
D  33  Y 411
A  34  I 412
Q  35  R 413
A  36  Y 414
V  37  G 415
E  44  G 422
E  45  A 423
T  46  I 424
A  47  M 425
F  48  N 426
V  49  G 427
L  50  I 428
D  51  S 429
Y  52  A 430
F  53  F 431
G  54  G 432
Q  65  N 434
A  66  Y 435
E  67  K 436
G  68  P 437
A  69  Y 438
K  70  G 439
Q  71  G 440
V  72  T 441
I  73  F 442
L  74  L 443
T  75  N 444
D  76  F 445
H  77  V 446
N  78  S 447
E  79  Y 448
F  80  A 449
Q  81  A 450
Q  82  A 452
S  83  V 453
I  84  R 454
A  85  L 455
D  86  S 456
I  87  A 457
R  88  L 458
E  89  S 459
V  90  G 460
E  91  H 461
V  92  V 463
V  93  I 464
E  94  W 465
V  95  V 466
V  96  A 467
D  97  T 468
H  98  H 469
H  99  D 470
N 103  L 487
F 104  A 488
E 105  H 489
T 106  F 490
A 107  R 491
P 109  I 496
L 110  Q 497
Y 111  V 498
M 112  W 499
R 113  R 500
L 114  P 501
E 115  A 502
P 116  D 503
V 117  G 504
G 118  N 505
S 119  E 506
A 120  V 507
S 121  S 508
S 122  A 509
I 123  A 510
V 124  Y 511
Y 125  K 512
R 126  N 513
L 127  S 514
Y 128  L 515
K 129  E 516
P 136  K 518
K 137  H 519
E 138  T 520
I 139  P 521
A 140  S 522
G 141  I 523
V 142  I 524
M 143  A 525
L 144  L 526
S 145  S 527
G 146  R 528
TER
PARENT 1trk_A
D 204  K 544
A 205  G 545
K 206  G 546
T 207  Y 547
F 208  V 548
E 209  L 549
L 210  Q 550
N 211  D 551
G 212  V 552
S 213  A 553
Q 214  N 554
V 215  P 555
R 216  D 556
V 217  I 557
A 218  I 558
Q 219  L 559
V 220  V 560
N 221  A 561
T 222  T 562
R 231  E 565
Q 232  V 566
N 233  S 567
E 234  L 568
I 235  S 569
E 236  V 570
E 237  E 571
A 238  A 572
I 239  A 573
K 240  K 574
A 241  T 575
S 242  L 576
Q 243  A 577
A 244  A 578
A 245  K 579
N 246  N 580
G 247  I 581
Y 248  K 582
S 249  A 583
D 250  R 584
F 251  V 585
V 252  V 586
L 253  S 587
M 254  L 588
I 258  L 606
L 259  P 607
N 260  D 608
S 261  N 609
N 262  V 610
S 263  P 611
E 264  I 612
I 265  M 613
L 266  S 614
A 267  V 615
L 268  E 616
G 269  V 617
N 270  L 618
N 271  A 619
T 272  T 620
D 273  T 621
K 274  C 622
A 278  Y 626
F 279  A 627
N 280  H 628
F 281  Q 629
T 282  S 630
L 283  F 631
K 284  G 632
TER
END

