
PFRMAT AL
TARGET T0094
AUTHOR 4216-9015-4014
REMARK Predictor remarks
METHOD CASP4 submission
METHOD 
METHOD Work by Kelley LA, MacCallum RM & Sternberg MJE
METHOD Biomolecular Modelling Laboratory
METHOD Imperial Cancer Research Fund
METHOD 44 Lincoln's Inn Fields
METHOD London WC2A 3PX, England 
METHOD Tel +44-(0)20-7269-3565 / 3242
METHOD FAX +44-(0)20-7269-3534
METHOD
METHOD Initial submission to the 3D-PSSM server returned a 
METHOD Ferredoxin-like fold at rank 4. Higher ranked folds
METHOD were dismissed due to incompatibilities of secondary structure elements.
METHOD The ferredoxin-like fold is known to contain RNA binders, which
METHOD is a possible related function for CPDase (see below).
METHOD Using the paper by Nasr F (Nucleic Acids Res 2000 Apr 15;28(8):1676-83)
METHOD we built an alignment from aligned RNA ligases from
METHOD a Pfam-B family (LIGT_ECOLI) and the target using CLUSTALW.
METHOD Submitting the 1st half of this alignment to the 3D-PSSM server
METHOD returned several high ranking hits to Ferredoxin-like folds.
METHOD The significance of the disulphides and the Histidine-containing  
METHOD motifs is not clear.
METHOD 3D-PSSM server:
METHOD http://www.bmm.icnet.uk/~3dpssm/
METHOD Kelley LA, MacCallum RM & Sternberg MJE (2000).
METHOD Enhanced Genome Annotation using Structural Profiles
METHOD in the Program 3D-PSSM. J. Mol. Biol. 299(2), 501-522.
METHOD 
METHOD Manual adjustments were made to the 3D-PSSM alignment to move   
METHOD gaps into coil regions to preserve the continuity of 
METHOD secondary structure elements.
METHOD 
MODEL 1
PARENT 1urn_A
M    1 P 4
E    2 E 5
E    3 T 6
V    4 R 7
K    5 P 8
K    6 N 9
D    7 H 10
V    8 T 11
Y    9 I 12
S   10 Y 13
V   11 I 14
W   12 N 15
A   13 N 16
L   14 L 17
P   15 N 18
D   16 E 19
E   17 K 20
E   18 I 21
S   19 K 22
E   20 K 23
P   21 D 24
R   22 E 25
F   23 L 26
K   24 K 27
K   25 K 28
L   26 S 29
M   27 L 30
E   28 H 31
A   29 A 32
L   30 I 33
R   31 F 34
S   32 S 35
E   33 Q 39
F   34 I 40
T   35 L 41
G   36 D 42
P   37 I 43
R   38 L 44
F   39 V 45
V   40 S 46
P   41 R 47
H   42 M 51
V   43 R 52
T   44 G 53
V   45 Q 54
A   46 A 55
V   47 F 56
S   48 V 57
A   49 I 58
Y   50 F 59
L   51 K 60
T   52 E 61
A   53 V 62
D   54 S 63
E   55 S 64
A   56 A 65
K   57 T 66
K   58 N 67
M   59 A 68
F   60 L 69
E   61 R 70
S   62 S 71
A   63 M 72
C   64 Q 73
D   65 G 74
G   66 F 75
L   67 P 76
K   68 F 77
A   69 D 79
Y   70 K 80
T   71 P 81
A   72 M 82
T   73 R 83
V   74 I 84
D   75 Q 85
R   76 Y 86
V   77 A 87
S   78 K 88
T   79 T 89
G   80 D 90
T   81 S 91
F   82 D 92
F   83 I 93
F   84 I 94
Q   85 A 95
C   86 K 96
V   87 M 97
TER
END

