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The structural motif discovery method presented herein is general and can be …


Biology Articles » Biochemistry » Protein Biochemistry » Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites » Tables

Tables
- Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites

Table 1

The letter and secondary structural element (SSE) frequency distributions and 2-sample T-tests of first-and second-shell amino acid residues vs. all amino acid residues in the Mg2+-proteins


1st-shell vs. all residues
2nd-shell vs. all residues
Letter, xa
νx,1/νx, allb
T-testc
p-valuec,d
νx,2/νx, alle
T-testc
p-valuec,d
a
1.47
1.4037
0.0802
0.57
2.4731
0.0067
b
1.86
2.7909
0.0027
1.20
1.2200
0.1113
c
0.56
2.0160
0.0219
0.50
4.3510

d
1.23
1.7376
0.0412
1.23
3.1829
0.0008
e
1.46
1.0111
0.1560
2.03
4.1825

f
1.47
1.9389
0.0263
1.70
5.4060

g
1.15
0.2494
0.4015
1.18
0.5381
0.2953
h
5.29
9.3752

1.19
0.7921
0.2142
i
0
1.8928
0.0292
1.34
1.1910
0.1168
j
2.21
1.6156
0.0531
1.54
1.3401
0.0901
k
1.40
1.4992
0.0669
1.60
4.1820

l
0.76
0.9209
0.1786
1.08
0.5978
0.275
m
0.52
2.9377
0.0017
0.74
5.2192

n
0.53
1.1306
0.1291
0.88
0.5208
0.3013
o
1.52
1.4066
0.0798
0.35
3.3637
0.0004
p
0
3.1174
0.0009
0.77
1.3204
0.0934
SSE, x






Loop
1.56
2.5575
0.0053
1.47
2.1874
0.0144
β-strands
1.30
1.0780
0.1405
1.34
1.2170
0.1118
α-helices
0.47
3.6454
0.0002
0.51
3.3621
0.0004

a16-letter structural alphabet defined by de Brevern and co-workers (see Methods and original reference) [6]. bThe ratio of the letter/SSE 'x' frequency of first-shell amino acid residues to that of all amino acid residues in the 70 Mg2+ proteins. cThe statistical analyses were carried out using the package, SAS/STAT version 8 (SAS Institute, NC). dP-values eThe ratio of the letter/SSE 'x' frequency of second-shell amino acid residues to that of all amino acid residues in the 70 Mg2+ proteins.

Dudev et al. BMC Bioinformatics 2007 8:106   doi:10.1186/1471-2105-8-106

Table 2

1st-shell structural motifs in Mg2+-proteins

Motifa
PDB code
Mg2+ -Ligands
CATH numberb
Functional Groupc
EC coded
e(24–47)h(24)k
1SJC
D189, E214, D239
3.20.20.120
Lyasee, Isomerasef
-

1TKK
D191, E219, D244
3.20.20.120
Isomerasef
-

2AKZ
D244, E292, D317
-
Lyasee
4.2.1.11






f(1)h(109–349)b
1O08
D1008, D1010, D1170
3.40.50.1000
Isomerasef
5.4.2.6

1U7P
D11, D13, D123
NYC
Hydrolaseg
-

1WPG
D351, T353, D703
3.40.50.1000
Hydrolaseg
3.6.3.8

2B82
D44, D46, D167
3.40.50.1000
Hydrolaseg
3.1.3.2

2C4N
D9, D11, D201
NYC
Hydrolaseg
-






f(2)h(126–158)m
1KA1
D142, D145, D294
3.30.540.10
Hydrolaseg
3.1.3.7

1NUY
D1118, D1121, E1280
3.30.540.10+ 3.40.190.80
Hydrolaseg
3.1.3.11

2BJI
E1090, D1093, D1220
3.30.540.10+ 3.40.190.80
Hydrolaseg
3.1.3.25






k(26–29)h(1)a
1ITZ
D168, N198, I200
3.40.50.970
Transferaseh
2.2.1.1

1POX
D447, N474, Q476
3.40.50.970+ 3.40.50.1220
Oxidoreductasei
1.2.3.3

1UMD
D175, N204, Y206
3.40.50.970
Oxidoreductasei
1.2.4.4

1ZPD
D440, N467, G469
3.40.50.970
Lyasee
4.1.1.1

2C3M
D963, T991, V993
3.40.50.970
Oxidoreductasei
1.2.7.1

aThe number in parentheses indicates the number of residues separating the letters corresponding to the Mg2+-bound residues. bThe CATH code of the domain containing the Mg2+-ligands; a dash implies that no domain could be assigned to the PDB entry, while NYC means the protein has not yet been chopped. cThe functional group from the PDB header. dThe enzyme class from PDBsum [25]; a dash means no EC code was found. eLyases (EC4---) catalyze C-C/O/N and other bond cleavage; e.g., RCOCOOH → RCOH + CO2. fIsomerases (EC5---) catalyze geometric changes within a molecule. gHydrolases (EC3---) catalyze hydrolytic bond cleavage: AB + H2O → AOH + BH. hTransferases (EC2---) catalyze AB + C → A + BC. iOxidoreductases (EC1---) catalyze oxido-reductions: AH + B → A + BH (reduced) and A + O → AO (oxidized).

Dudev et al. BMC Bioinformatics 2007 8:106   doi:10.1186/1471-2105-8-106


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