Chapter 4. Conclusions and Future Works
4.2 Applications and Future Works
Since the discovered novel motifs are more important to the ATP-binding, the novel
motifs can then be used to predict the ATP-binding property of proteins not complexed with
ATPs or even protein sequences that the structures are not solved yet.
With the fast protein-ATP complex clustering method and the protein-ligand interaction
analyses proposed in this work, we can also apply the same process to protein-ligand
complexes of any other ligand. Therefore, we can discover more potential novel
ligand-binding motifs that essential for the ligand-binding. Moreover, we can construct a
ligand-binding motif database and provide some services for searching proteins that could be
bound by a given ligand or ligands that probably bind to a given protein. However, since the
lack of evidence of the novel ligand-binding motifs currently, the newly discovered motifs
should be carefully validated in the future days.
Table 1. The accuracy for each cluster
Cida # Members # Members having SCOPb # Correct Clustered Accuracy
1 1 1 1 100%
Cida # Members # Members having SCOPb # Correct Clustered Accuracy
51 1 1 1 100%
52 4 3 1 33%
53 4 4 2 50%
54 1 1 1 100%
55 1 1 1 100%
56 1 1 1 100%
57 3 3 3 100%
58 16 9 7 78%
59 6 4 4 100%
60 7 7 7 100%
61 3 1 1 100%
62 3 2 2 100%
63 11 7 7 100%
64 8 4 4 100%
65 1 0 - -
66 1 1 1 100%
67 1 1 1 100%
68 5 4 4 100%
69 1 1 1 100%
70 1 1 1 100%
a The serial identification of clusters.
b The number of cluster members with domain records in SCOP.
Table 2. The cluster results after eliminating homologues
Cida Repb Chain SCOP Families of
Contact Domains c EC Protein Name
1 4at1B 4at1B d.58.2.1 (21) 2.1.3.2 Aspartate Carbamoyltransferase
2 2c01X 2c01X 3.1.27.5 Nonsecretory Ribonuclease
3 2aruA 2aruA 6.3.2.- Lipoate-Protein Ligase A
4 2aqxA 2aqxA 2.7.1.127 Inositol 1,4,5-Trisphosphate 3-Kinase B 5 8icnA 8icnA d.218.1.2 (15) 2.7.7.7 DNA Polymerase Beta
6 1z0sA 1z0sA 2.7.1.23 Polyphosphate/ATP-NAD Kinase
7 1yp3A 1yp3A 2.7.7.27 Glucose-1-Phosphate Adenylyltransferase Small Subunit (ADP-Glucose Synthase)
8 1y56A 1y56A 1.5.99.8 L-Proline Dehydrogenase
9 1xdnA 1xdnA RNA Editing Ligase Mp52
10 1wklB 1wklB 2.7.4.6 Nucleotide Diphosphate Kinase 11 1vjcA 1vjcA c.86.1.1 (26) 2.7.2.3 Phosphoglycerate Kinase
3pgk_ c.86.1.1 (28) 2.7.2.3 Phosphoglycerate Kinase
12 2gnkA 2gnkA d.58.5.1 (17) Nitrogen Regulatory Protein
13 1v3sA 1v3sA Nitrogen Regulatory Protein Pii
14 1twaA 1twaA 2.7.7.6 DNA-Directed RNA Polymerase II Largest Subunit
15 1tc0A 1tc0A d.122.1.1 (25) Endoplasmin
16 1qhxA 1qhxA c.37.1.3 (28) 2.7.1.- Chloramphenicol Phosphotransferase
17 1obgA 1obgA d.143.1.1 (13) 6.3.2.6 Phosphoribosylamidoimidazole-Succinocarboxamide Synthase 18 1obdA 1obdA d.143.1.1 (23) 6.3.2.6 Phosphoribosylamidoimidazole-Succinocarboxamide Synthase 19 1o93B 1o93B d.130.1.1 (14) 2.5.1.6 S-Adenosylmethionine Synthetase
20 1o93A 1o93A d.130.1.1 (16) 2.5.1.6 S-Adenosylmethionine Synthetase
21 1yfrA 1yfrA 6.1.1.7 Alanyl-tRNA Synthetase
22 1n48A 1n48A e.8.1.7 (22) DNA Polymerase IV
23 1mo8A 1mo8A d.220.1.1 (24) Sodium/Potassium-Transporting Atpase Alpha-1
24 1mjhA 1mjhA c.26.2.4 (32) (unknown)
25 1miwA 1miwA d.218.1.4 (17), a.173.1.1 (11) tRNA Cca-Adding Enzyme 26 1w7aB 1w7aB c.37.1.12 (28) DNA Mismatch Repair Protein Muts 27 1ko5A 1ko5A c.37.1.17 (23) 2.7.1.12 Gluconate Kinase
28 1r8bA 1r8bA d.218.1.7 (23), a.160.1.3 (6), d.58.16.2 (10)
tRNA Nucleotidyltransferase
29 1jwaB 1jwaB c.111.1.1 (29) Molybdopterin Biosynthesis MoeB Protein
1r4nB c.111.1.2 (30) Ubiquitin-Activating Enzyme E1C
1y8qB Ubiquitin-Like 2 Activating Enzyme E1B
1zfnA 2.7.7.- Adenylyltransferase THIF
30 1xscA 1jknA d.113.1.1 (33) 3.6.1.17 Diadenosine 5',5'''-P1,P4-Tetraphosphate Hydrolase
1su2A d.113.1.1 (21) Mutt/Nudix Family Protein
1vc9A HB8 Ap6A Hydrolase
1xscA 3.6.1.17 Bis(5'-Nucleosyl)-Tetraphosphatase
31 1jjvA 1jjvA c.37.1.1 (20) 2.7.1.24 Dephospho-CoA Kinase
1uf9C c.37.1.1 (24) (unknown)
32 1jagA 1jagA c.37.1.1 (33) 2.7.1.113 Deoxyguanosine Kinase
33 3r1rA 3r1rA a.98.1.1 (19) 1.17.4.1 Ribonucleotide Reductase R1 Protein 34 1hp1A 1hp1A d.114.1.1 (14) 3.1.3.5, 3.6.1.45 5'-Nucleotidase
35 1hi1A 1hi1A e.8.1.6 (16) RNA Polymerase
36 1pj4A 1pj4A c.2.1.7 (22), c.58.1.3 (7) 1.1.1.39 NAD-Dependent Malic Enzyme, Mitochondrial 37 1n77A 1gtrA c.26.1.1 (29) 6.1.1.18 Glutaminyl-tRNA Synthetase
1n77A c.26.1.1 (28) 6.1.1.17 Glutamyl-tRNA Synthetase
Cida Repb Chain SCOP Families of
Contact Domains c EC Protein Name
38 1g5tA 1g5tA c.37.1.11 (18) 2.5.1.17 COB(I)Alamin Adenosyltransferase
39 1xdpA 1xdpA 2.7.4.1 Polyphosphate Kinase
40 1gn8A 1f9aA c.26.1.3 (28) NMN Adenylyltransferase
1gn8A c.26.1.3 (33) 2.7.7.3 Phosphopantetheine Adenylyltransferase 1yunA 2.7.7.18 Nicotinate-Nucleotide Adenylyltransferase
41 1xexA 1f2uA c.37.1.12 (21) RAD50 ABC-Atpase
1xexA SMC Protein
42 1kvkA 1kvkA d.14.1.5 (29) Mevalonate Kinase
43 1yidB 1h3eA c.26.1.1 (32) 6.1.1.1 Tyrosyl-tRNA Synthetase 1m83A c.26.1.1 (36) 6.1.1.2 Tryptophanyl-tRNA Synthetase
1yidB 6.1.1.2 Tryptophanyl-tRNA Synthetase
2a84A 6.3.2.1 Pantoate--Beta-Alanine Synthetase
44 1nsyA 1nsyA c.26.2.1 (27) 6.3.5.1 NAD Synthetase
45 1r9tB 1r9tB 2.7.7.6 DNA-Directed RNA Polymerase II 46 1fmwA 1fmwA c.37.1.9 (32) Myosin II Heavy Chain
47 1sx3A 1sx3A Groel Protein
48 2bu2A 1tilA d.122.1.3 (35) 2.7.1.37 Anti-Sigma Factor Spoiiab
1y8pA 2.7.1.99 [Pyruvate Dehydrogenase [Lipoamide]] Kinase Isozyme 3 2bu2A 2.7.1.99 Pyruvate Dehydrogensae Kinase Isoenzyme 2
49 1n5iA 1n5iA c.37.1.1 (10) Thymidylate Kinase
50 1e2qA 1e2qA c.37.1.1 (21) 2.7.4.9 Thymidylate Kinase
51 1dy3A 1dy3A d.58.30.1 (27) 2.7.6.3 7,8-Dihydro-6-Hydroxymethylpterinpyrophosphokinase (Pyrophosphorylase, Pppk)
52 2f02A 1esqA c.72.1.2 (27) 2.7.1.50 Hydroxyethylthiazole Kinase 1lhrA c.72.1.5 (29) 2.7.1.35 Pyridoxal Kinase
1v1bA c.72.1.1 (34) 2-Keto-3-Deoxygluconate Kinase
2f02A 2.7.1.144 Tagatose-6-Phosphate Kinase
53 1dv2A 1dv2A d.142.1.2 (28) 6.3.4.14 Biotin Carboxylase
1kj8A d.142.1.2 (30) 2.1.2.- Phosphoribosylglycinamide Formyltransferase 2
1i7lA d.142.1.3 (32) Synapsin II
1pk8A d.142.1.3 (29) Synapsin I
54 1d9zA 1d9zA c.37.1.19 (23) DNA Repair Protein UVRB 55 1bcpF 1bcpF b.40.2.1 (9) 2.4.2.- Pertussis Toxin 56 1bcpE 1bcpE b.40.2.1 (13) 2.4.2.- Pertussis Toxin
57 1h8hA 1e79A c.37.1.11 (17) 3.6.1.34 ATP Synthase Alpha Chain Heart Isoform (Bovine Mitochondrial F1-Atpase)
1h8hA c.37.1.11 (19) 3.6.1.34 ATP Synthase Alpha Chain Heart Isoform 1tf7A c.37.1.11 (23) Circadian Clock Protein KAIC 58 1gol_ 1atpE d.144.1.7 (33) 2.7.1.37 cAMP-Depedent Protein Kinase (CAPK)
1b38A d.144.1.7 (30) 2.7.1.37 Cell Division Protein Kinase 2 1ol6A d.144.1.7 (26) 2.7.1.37 Serine/Threonine Kinase 6 1csn_ d.144.1.7 (29) 2.7.1.- Casein Kinase-1 1phk_ d.144.1.7 (31) 2.7.1.38 Phosphorylase Kinase 1gol_ d.144.1.7 (22) 2.7.1.- Extracellular Regulated Kinase 2 1q97A d.144.1.7 (29) 2.7.1.- Sr Protein Kinase
1e8xA d.144.1.4 (26) 2.7.1.137 Phosphatidylinositol 3-Kinase Catalytic Subunit
1tqpA d.144.1.9 (28) RIO2 Serine Protein Kinase
1zp9A RIO1 Kinase
1s9iA Dual Specificity Mitogen-Activated Protein Kinase Kinase 2 1s9jA Dual Specificity Mitogen-Activated Protein Kinase Kinase 1
1u5rA Serine/Threonine Protein Kinase Tao2
1ua2A 2.7.1.37 Cell Division Protein Kinase 7 1zydA 2.7.1.37 Serine/Threonine-Protein Kinase GCN2 2biyA 2.7.1.37 3-Phosphoinositide Dependent Protein Kinase-1 59 1eqyA 1e4gT c.55.1.1 (33) Cell Division Protein FTSA
1eqyA c.55.1.1 (36) Alpha-Actin
1nge_ c.55.1.1 (36) 3.6.1.3 Heat-Shock Cognate 70Kd Protein
1yagA c.55.1.1 (37) Actin
1tyqA Actin-Related Protein 3
1tyqB Actin-Related Protein 2
Cida Repb Chain SCOP Families of
Contact Domains c EC Protein Name
60 1b76A 1aszA d.104.1.1 (22) 6.1.1.12 Aspartyl tRNA Synthetase 1b76A d.104.1.1 (29) 6.1.1.14 Glycyl-tRNA Synthetase 1b8aA d.104.1.1 (26) 6.1.1.12 Aspartyl-tRNA Synthetase 1e24A d.104.1.1 (29) 6.1.1.6 Lysyl-tRNA Synthetase 1h4qA d.104.1.1 (27) 6.1.1.15 Prolyl-tRNA Synthetase 1kmnA d.104.1.1 (30) 6.1.1.21 Histidyl-tRNA Synthetase 1nyrA d.104.1.1 (28) 6.1.1.3 Threonyl-tRNA Synthetase 1 61 1ayl_ 1ayl_ c.91.1.1 (37) 4.1.1.49 Phosphoenolpyruvate Carboxykinase
1xkvA 4.1.1.49 Phosphoenolpyruvate Carboxykinase
1ytmA 4.1.1.49 Phosphoenolpyruvate Carboxykinase
62 2bekA 1a82_ c.37.1.10 (29) 6.3.3.3 Dethiobiotin Synthetase 1g21E c.37.1.10 (31) 1.18.6.1 Nitrogenase Iron Protein
2bekA Segregation Protein SOJ
63 1b0uA 1b0uA c.37.1.12 (19) ABC Transporter (Histidine Permease)
1f2uB c.37.1.12 (19) RAD50 ABC-Atpase
1ji0A c.37.1.12 (21) ABC Transporter
1l2tA c.37.1.12 (22) ABC Transporter
1mv5A c.37.1.12 (17) Multidrug Resistance ABC Transporter ATP-Binding And Permease Protein
1q12A c.37.1.12 (31) Maltose/Maltodextrin Transport ATP-Binding Protein Malk 1r0xA c.37.1.12 (21) Cystic Fibrosis Transmembrane Conductance Regulator (CFTR)
1vciA Sugar-Binding Transport ATP-Binding Protein
1xefA Alpha-Hemolysin Translocation ATP-Binding Protein HLYB
1xexB SMC Protein
1xmiA 3.6.3.49 Cystic Fibrosis Transmembrane Conductance Regulator 64 1nsf_ 1do0A c.37.1.20 (29) Chaperone (Heat Shock Locus U)
1g3iA c.37.1.20 (29) ATP-Dependent HSLU Protease
1j7kA c.37.1.20 (31) Holliday Junction DNA Helicase Ruvb
1nsf_ c.37.1.20 (26) N-Ethylmaleimide Sensitive Factor
1ojlE Transcriptional Regulatory Protein Zrar
1svmA Large T Antigen
2a5yB CED-4
2c96A PSP Operon Transcriptional Activator
65 1z7eA 1z7eA Protein ArnA
66 1qhgA 1qhgA c.37.1.19 (25) ATP-Dependent Helicase Pcra 67 1ii0A 1ii0A c.37.1.10 (29) 3.6.3.16 Arsenical Pump-Driving Atpase 68 1xngA 1ee1A c.26.2.1 (33) 6.3.5.1 NH3-Dependent NAD+ Synthetase
1j1zA c.26.2.1 (24) 6.3.4.5 Argininosuccinate Synthetase 1kp2A c.26.2.1 (28) 6.3.4.5 Argininosuccinate Synthetase
1mb9A c.26.2.1 (33) Beta-Lactam Synthetase
1xngA 6.3.1.5 NH(3)-Dependent NAD(+) Synthetase
69 1a49A 1a49A c.1.12.1 (24), b.58.1.1 (11) 2.7.1.40 Pyruvate Kinase
70 1a0i_ 1a0i_ d.142.2.1 (22) 6.5.1.1 DNA Ligase a The serial identification of clusters.
b The representative protein chain of the `Cid’-th cluster.
c The SCOP families of the contact domains. The numbers in the parentheses are the number of contact residues belonging to the contact SCOP domain.
Table 3. Statistics on interaction similarity of non-singleton clusters
Interaction Similarity
Cid Average Std. Dev. Min Max
# ≥ 50% Interactional Conserved Positions
11 22.20% 0.00% 22.20% 22.20% 2
29 32.50% 10.00% 16.70% 44.40% 4
30 10.50% 11.50% 0.00% 28.60% 5
31 58.30% 0.00% 58.30% 58.30% 7
37 33.30% 0.00% 33.30% 33.30% 3
40 12.80% 3.40% 8.30% 16.70% 5
41 57.10% 0.00% 57.10% 57.10% 8
43 28.60% 13.10% 6.70% 46.20% 8
48 36.70% 6.80% 27.30% 42.90% 7
52 25.00% 8.80% 10.00% 37.50% 6
53 29.10% 20.10% 8.30% 55.60% 11
57 53.90% 11.40% 45.50% 70.00% 8
58 38.90% 16.80% 8.30% 100.00% 5
59 46.60% 21.80% 14.30% 91.70% 11
60 41.00% 11.80% 14.30% 70.00% 6
61 63.90% 13.30% 50.00% 81.80% 9
62 51.90% 14.30% 37.50% 71.40% 11
63 39.10% 31.40% 0.00% 100.00% 6
64 38.50% 14.00% 13.30% 62.50% 8
68 32.70% 17.80% 6.70% 66.70% 6
Table 4. Statistics on sequence identity of non-singleton clusters before eliminating
a The serial identification of clusters.
b The accuracy compared to SCOP. Clusters with no contact SCOP domain found are marked as a dash.
Table 5. Statistics on sequence identity of non-singleton clusters after eliminating
a The serial identification of clusters.
b The SCOP families of the contact domains.
(a)
(b)
(c) (d)
Figure 1. Properties of ATP. (a) Molecular structure and chemical groups of ATP. The atoms are labeled according to the IUPAC_IUB JCBN naming system. (b) The ATP structure and the hydrogen bonds to the surrounding residues in 1atp. ATP acts as a hydrogen bond donor (N6) and a hydrogen bond acceptor (N1, N3, N7, O3*, O4*, O2*, and oxygen atoms on phosphates). (c) The π-π stacking between the π rings of ATP and aromatic amino acids, Phe, Tyr, and Trp. (d) The cation-π interaction between the π ring of ATP and positively charged amino acids, Arg and Lys.
Figure 2. The framework of this research. We first get the whole list of PDB structures complexed with ATPs and extract the binding pockets. Then, we queried each chain to a protein structure similarity search engine, called 3D-BLAST and filtered the results with CE. After that, we applied the simple clustering methods by simply merging clusters with common members. The interactions are identified after the clustering.
Protein Structure Similarity Search for each chain
Filtering the Results with CE Binding Site
Extraction List chains that bind ATP
Protein-Ligand Interaction Analysis
Interaction Identification Simple Clustering
Clusters
Homologues Elimination
(a)
(b)
Figure 3. The multiple structure alignment of ATP binding-pockets in the cluster 29. (a) The close view of ATP-binding pockets in the cluster 29. (b) The multiple structure alignment and interaction profile of the cluster 29. The contact residues are shown in uppercases while the others in lowercases. The hydrogen bonds (represented by bars, `|’) to the phosphate groups are highly conserved within the cluster. Moreover, we also identified a potential novel motif, [IV]-G-[AL]-G-G-[IL]-G-X(17)-[28]-D-[MFLD]-D-[TD]-[IV]-[SDH]-[LV]-S-N-L-[NQ]-R-Q-X(11)-K (the red box), called C29_PAT, in that area. We believe that C29_PAT can be a signature for ubiquitin-activating related proteins and adenylyltransferases, which are the members of cluster 29.
C29_PAT
(a)
(b) (c)
(d)
Figure 4. The potential motifs in the cluster 59. (a) The multiple structure alignment of the cluster 59 with showing the potential motifs, C59_PAT_1, C59_PAT_2, and C59_PAT_3. (b) (c) (d) The superposition of the ATP-binding pockets with showing the C59_PAT_1, C59_PAT_2, and C59_PAT_3 as sticks, respectively.
C59_PAT_1 C59_PAT_2 C59_PAT_3
C59_PAT_1
C59_PAT_2
C59_PAT_3
(a)
(b)
Figure 5. The CE structural alignments and the interaction profile of the ATP-binding pockets of the cluster 30. (a) The superposition of ATP-binding protein chains in the cluster 30. (b) The multiple structure alignment and interaction profile in ATP-binding pockets of the cluster 30. From the figures
(a)
(b)
Figure 6. An example of structural binding pocket alignment of the cluster 58. (a) The superposition of ATP-binding protein chains in the cluster 58. (b) The multiple structure alignment and interaction profile in ATP-binding pockets of the cluster 58. The superposition of the ATP-binding pocket structures in 9 protein chains, which have records in the SCOP, of the cluster 58. We can see that the hydrogen bond pattern around the adenine groups is strongly conserved among the cluster.
(a) (b)
(c)
(d)
Figure 7. An example of structural binding pocket alignment of the cluster 53. (a) The ATP-binding pockets and the hydrogen bonds in protein chains of the cluster 53.
(b) The superposition of the protein chains in the cluster 53. The protein chains colored in cyan, magenta, yellow, and salmon red are 1dv2A, 1pk8A, 1j7lA, and 1kj8A, respectively. (c) The multiple structure alignment and the interaction profile of the cluster 53, with showing the `shifting’ region. (d) the superposition of ATP and the residues interacting with ATP in 1dv2A and 1kj8A from two different angles. We can see that the ATP structure is not well superposed to the others but the hydrogen bonds are somehow conserved. The error of superposing 1kj8A causes the shift of the non-bonded interaction pattern in the multiple structure alignment of the cluster.
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35. Sali, A., et al., From comparisons of protein sequences and structures to protein modelling and design. Trends in Biochemical Sciences, 1990. 15(6): p. 235-240.
36. Flaherty, K.M., et al., Structural basis of the 70-kilodalton heat shock cognate protein ATP hydrolytic activity. II. Structure of the active site with ADP or ATP bound to wild type and mutant ATPase fragment. The Journal of Biological Chemistry, 1994.
269(17): p. 12899-12907.
Appendix A.
The 486 ATP-binding protein chains and their names, EC numbers, and SCOP families involving in ATP-binding.
Cid Rep. Chain # cRes Contact SCOP
Domain Families EC Protein Name
1 4at1B 4at1B 21 d.58.2.1 2.1.3.2 Aspartate Carbamoyltransferase 4at1D 19 d.58.2.1 (19) 2.1.3.2 Aspartate Carbamoyltransferase 7at1B 20 d.58.2.1 (20) 2.1.3.2 Aspartate Carbamoyltransferase
2 2c01X 2c01X 24 3.1.27.5 Nonsecretory Ribonuclease
3 2aruA 2aruA 39 6.3.2.- Lipoate-Protein Ligase A
4 2aqxA 2aqxA 30 2.7.1.127 Inositol 1,4,5-Trisphosphate 3-Kinase B 2aqxB 31 2.7.1.127 Inositol 1,4,5-Trisphosphate 3-Kinase B
5 8icnA 8icnA 15 d.218.1.2 (15) 2.7.7.7 DNA Polymerase Beta
6 1z0sA 1z0sA 28 2.7.1.23 Polyphosphate/ATP-NAD Kinase 1z0sB 28 2.7.1.23 Polyphosphate/ATP-NAD Kinase 1z0sC 28 2.7.1.23 Polyphosphate/ATP-NAD Kinase 1z0sD 29 2.7.1.23 Polyphosphate/ATP-NAD Kinase
7 1yp3A 1yp3A 33 2.7.7.27 Glucose-1-Phosphate Adenylyltransferase Small Subunit (ADP-Glucose Synthase)
1yp3C 35 2.7.7.27 Glucose-1-Phosphate Adenylyltransferase Small Subunit (ADP-Glucose Synthase)
8 1y56A 1y56A 41 1.5.99.8 L-Proline Dehydrogenase
9 1xdnA 1xdnA 28 RNA Editing Ligase Mp52
10 1wklB 1wklB 19 2.7.4.6 Nucleotide Diphosphate Kinase
11 1vjcA 1vjcA 26 c.86.1.1 (26) 2.7.2.3 Phosphoglycerate Kinase 1vjdA 34 c.86.1.1 (34) 2.7.2.3 Phosphoglycerate Kinase 3pgk_ 28 c.86.1.1 (28) 2.7.2.3 Phosphoglycerate Kinase
12 2gnkA 2gnkA 17 d.58.5.1 (17) Nitrogen Regulatory Protein
13 1v3sA 1v3sA 30 Nitrogen Regulatory Protein Pii 1v3sB 29 Nitrogen Regulatory Protein Pii 1v3sC 28 Nitrogen Regulatory Protein Pii
14 1twaA 1twaA 8 2.7.7.6 DNA-Directed RNA Polymerase II Largest Subunit 1twhA 7 2.7.7.6 DNA-Directed RNA Polymerase II Largest Subunit
15 1tc0A 1tc0A 26 d.122.1.1 (25) Endoplasmin 1tc0B 23 d.122.1.1 (23) Endoplasmin
16 1qhxA 1qhxA 28 c.37.1.3 (28) 2.7.1.- Chloramphenicol Phosphotransferase
17 1obgA 1obgA 13 d.143.1.1 (13) 6.3.2.6 Phosphoribosylamidoimidazole-Succinocarboxamide Synthase
18 1obdA 1obdA 23 d.143.1.1 (23) 6.3.2.6 Phosphoribosylamidoimidazole-Succinocarboxamide Synthase
19 1o93B 1o93B 14 d.130.1.1 (14) 2.5.1.6 S-Adenosylmethionine Synthetase 1o9tB 15 d.130.1.1 (15) 2.5.1.6 S-Adenosylmethionine Synthetase
20 1o93A 1o93A 16 d.130.1.1 (16) 2.5.1.6 S-Adenosylmethionine Synthetase 1o9tA 13 d.130.1.1 (12) 2.5.1.6 S-Adenosylmethionine Synthetase
21 1yfrA 1yfrA 22 6.1.1.7 Alanyl-tRNA Synthetase 1yfrB 22 6.1.1.7 Alanyl-tRNA Synthetase
23 1mo8A 1mo8A 24 d.220.1.1 (24) Sodium/Potassium-Transporting Atpase Alpha-1
24 1mjhA 1mjhA 32 c.26.2.4 (32) (Hypothetical) 1mjhB 32 c.26.2.4 (32) (Hypothetical)
25 1miwA 1miwA 28 d.218.1.4 (17), a.173.1.1 (11) tRNA Cca-Adding Enzyme 1miwB 28 d.218.1.4 (17), a.173.1.1 (11) tRNA Cca-Adding Enzyme
26 1w7aB 1w7aB 28 c.37.1.12 (28) DNA Mismatch Repair Protein Muts
27 1ko5A 1ko5A 23 c.37.1.17 (23) 2.7.1.12 Gluconate Kinase 1ko5B 25 c.37.1.17 (25) 2.7.1.12 Gluconate Kinase
28 1r8bA 1r8bA 39 d.218.1.7 (23), a.160.1.3 (6),
d.58.16.2 (10) tRNA Nucleotidyltransferase 1tfwB 27 d.218.1.7 (18), a.160.1.3 (9) 2.7.7.25 tRNA Nucleotidyltransferase
1tfwD 28 d.218.1.7 (18), a.160.1.3 (10) 2.7.7.25 tRNA Nucleotidyltransferase 1uevA 29 d.218.1.7 (20), a.160.1.3 (9) 2.7.7.25 tRNA Nucleotidyltransferase
29 1zfnA 1jwaB 29 c.111.1.1 (29) Molybdopterin Biosynthesis MoeB Protein 1r4nB 30 c.111.1.2 (30) Ubiquitin-Activating Enzyme E1C 1r4nD 29 c.111.1.2 (29) Ubiquitin-Activating Enzyme E1C 1r4nF 30 c.111.1.2 (30) Ubiquitin-Activating Enzyme E1C 1r4nH 28 c.111.1.2 (28) Ubiquitin-Activating Enzyme E1C
1y8qB 30 Ubiquitin-Like 2 Activating Enzyme E1B 1y8qD 32 Ubiquitin-Like 2 Activating Enzyme E1B 1y8rB 31 Ubiquitin-Like 2 Activating Enzyme E1B 1y8rE 31 Ubiquitin-Like 2 Activating Enzyme E1B 1zfnA 28 2.7.7.- Adenylyltransferase THIF 1zfnB 30 2.7.7.- Adenylyltransferase THIF 1zfnC 29 2.7.7.- Adenylyltransferase THIF 1zfnD 31 2.7.7.- Adenylyltransferase THIF
30 1vc9A 1jknA 33 d.113.1.1 (33) 3.6.1.17 Diadenosine 5',5'''-P1,P4-Tetraphosphate Hydrolase 1su2A 21 d.113.1.1 (21) Mutt/Nudix Family Protein
1su2B 24 d.113.1.1 (18) Mutt/Nudix Family Protein
1vc9A 22 HB8 Ap6A Hydrolase
1vc9B 21 HB8 Ap6A Hydrolase
1xscA 25 3.6.1.17 Bis(5'-Nucleosyl)-Tetraphosphatase
31 1jjvA 1jjvA 20 c.37.1.1 (20) 2.7.1.24 Dephospho-CoA Kinase 1uf9C 24 c.37.1.1 (24)
32 1jagD 1jagA 33 c.37.1.1 (33) 2.7.1.113 Deoxyguanosine Kinase
33 3r1rA 3r1rA 19 a.98.1.1 (19) 1.17.4.1 Ribonucleotide Reductase R1 Protein 3r1rB 20 a.98.1.1 (20) 1.17.4.1 Ribonucleotide Reductase R1 Protein
36 1pj4D 1gz3A 30 c.58.1.3 (7), c.2.1.7 (23) 1.1.1.38 NAD-Dependent Malic Enzyme 1gz3B 29 c.58.1.3 (7), c.2.1.7 (22) 1.1.1.38 NAD-Dependent Malic Enzyme
1pj4A 32 c.2.1.7 (22), c.58.1.3 (7) 1.1.1.39 NAD-Dependent Malic Enzyme, Mitochondrial 1pj4B 32 c.2.1.7 (22), c.58.1.3 (7) 1.1.1.39 NAD-Dependent Malic Enzyme, Mitochondrial 1pj4C 32 c.2.1.7 (22), c.58.1.3 (7) 1.1.1.39 NAD-Dependent Malic Enzyme, Mitochondrial 1pj4D 32 c.2.1.7 (22), c.58.1.3 (7) 1.1.1.39 NAD-Dependent Malic Enzyme, Mitochondrial
37 1qrsA 1gtrA 29 c.26.1.1 (29) 6.1.1.18 Glutaminyl-tRNA Synthetase 1n77A 28 c.26.1.1 (28) 6.1.1.17 Glutamyl-tRNA Synthetase 1n77B 29 c.26.1.1 (29) 6.1.1.17 Glutamyl-tRNA Synthetase 1qrsA 33 c.26.1.1 (33) 6.1.1.18 Glutaminyl-tRNA Synthetase 1qrtA 33 c.26.1.1 (33) 6.1.1.18 Glutaminyl-tRNA Synthetase 1qruA 30 c.26.1.1 (30) 6.1.1.18 Glutaminyl-tRNA Synthetase
38 1g64A 1g5tA 18 c.37.1.11 (18) 2.5.1.17 COB(I)Alamin Adenosyltransferase 1g64A 26 c.37.1.11 (25) 2.5.1.17 COB(I)Alamin Adenosyltransferase 1g64B 26 c.37.1.11 (24) 2.5.1.17 COB(I)Alamin Adenosyltransferase
39 1xdpB 1xdpA 33 2.7.4.1 Polyphosphate Kinase 1xdpB 34 2.7.4.1 Polyphosphate Kinase
40 1yunB 1f9aA 28 c.26.1.3 (28) NMN Adenylyltransferase 1f9aB 27 c.26.1.3 (27) NMN Adenylyltransferase 1f9aC 28 c.26.1.3 (28) NMN Adenylyltransferase 1f9aD 29 c.26.1.3 (29) NMN Adenylyltransferase 1f9aE 29 c.26.1.3 (29) NMN Adenylyltransferase 1f9aF 28 c.26.1.3 (28) NMN Adenylyltransferase
1gn8A 33 c.26.1.3 (33) 2.7.7.3 Phosphopantetheine Adenylyltransferase 1gn8B 32 c.26.1.3 (32) 2.7.7.3 Phosphopantetheine Adenylyltransferase 1yunA 25 2.7.7.18 Nicotinate-Nucleotide Adenylyltransferase 1yunB 27 2.7.7.18 Nicotinate-Nucleotide Adenylyltransferase
41 1f2uA 1f2uA 21 c.37.1.12 (21) RAD50 ABC-Atpase 1f2uC 20 c.37.1.12 (20) RAD50 ABC-Atpase
1xexA 23 SMC Protein
42 1kvkA 1kvkA 29 d.14.1.5 (29) Mevalonate Kinase
43 1mauA 1h3eA 32 c.26.1.1 (32) 6.1.1.1 Tyrosyl-tRNA Synthetase 1m83A 36 c.26.1.1 (36) 6.1.1.2 Tryptophanyl-tRNA Synthetase 1mauA 36 c.26.1.1 (36) 6.1.1.2 Tryptophanyl-tRNA Synthetase 1mawA 24 c.26.1.1 (24) 6.1.1.2 Tryptophanyl-tRNA Synthetase 1mawB 27 c.26.1.1 (27) 6.1.1.2 Tryptophanyl-tRNA Synthetase 1mawC 27 c.26.1.1 (27) 6.1.1.2 Tryptophanyl-tRNA Synthetase 1mawD 28 c.26.1.1 (28) 6.1.1.2 Tryptophanyl-tRNA Synthetase 1mawE 21 c.26.1.1 (21) 6.1.1.2 Tryptophanyl-tRNA Synthetase 1mawF 23 c.26.1.1 (23) 6.1.1.2 Tryptophanyl-tRNA Synthetase 1yidB 29 6.1.1.2 Tryptophanyl-tRNA Synthetase 2a84A 30 6.3.2.1 Pantoate--Beta-Alanine Synthetase
44 1nsyA 1nsyA 27 c.26.2.1 (27) 6.3.5.1 NAD Synthetase 1nsyB 26 c.26.2.1 (16) 6.3.5.1 NAD Synthetase
45 1twaB 1r9tB 8 2.7.7.6 DNA-Directed RNA Polymerase II
1twaB 10 2.7.7.6 DNA-Directed RNA Polymerase II 140 Kd Polypeptide
48 1tilA 1tidA 29 d.122.1.3 (29) 2.7.1.37 Anti-Sigma Factor Spoiiab 1tidC 37 d.122.1.3 (37) 2.7.1.37 Anti-Sigma Factor Spoiiab 1tilA 35 d.122.1.3 (35) 2.7.1.37 Anti-Sigma Factor Spoiiab 1tilC 35 d.122.1.3 (35) 2.7.1.37 Anti-Sigma Factor Spoiiab 1tilE 36 d.122.1.3 (36) 2.7.1.37 Anti-Sigma Factor Spoiiab
1y8pA 30 2.7.1.99 [Pyruvate Dehydrogenase [Lipoamide]] Kinase Isozyme 3
2bu2A 26 2.7.1.99 Pyruvate Dehydrogensae Kinase Isoenzyme 2
49 1n5iA 1n5iA 10 c.37.1.1 (10) Thymidylate Kinase
50 1e2qA 1e2qA 21 c.37.1.1 (21) 2.7.4.9 Thymidylate Kinase
51 1dy3A 1dy3A 27 d.58.30.1 (27) 2.7.6.3 7,8-Dihydro-6-Hydroxymethylpterinpyrophosphokinase (Pyrophosphorylase, Pppk)
52 1lhrA 1esqA 27 c.72.1.2 (27) 2.7.1.50 Hydroxyethylthiazole Kinase 1esqB 27 c.72.1.2 (27) 2.7.1.50 Hydroxyethylthiazole Kinase 1esqC 27 c.72.1.2 (27) 2.7.1.50 Hydroxyethylthiazole Kinase 1lhrA 29 c.72.1.5 (29) 2.7.1.35 Pyridoxal Kinase 1dv2B 30 d.142.1.2 (28) 6.3.4.14 Biotin Carboxylase 1i7lA 32 d.142.1.3 (32) Synapsin II 1i7lB 30 d.142.1.3 (29) Synapsin II
1kj8A 32 d.142.1.2 (30) 2.1.2.- Phosphoribosylglycinamide Formyltransferase 2 1kj8B 27 d.142.1.2 (26) 2.1.2.- Phosphoribosylglycinamide Formyltransferase 2 1kj9A 31 d.142.1.2 (30) 2.1.2.- Phosphoribosylglycinamide Formyltransferase 2 1kj9B 29 d.142.1.2 (28) 2.1.2.- Phosphoribosylglycinamide Formyltransferase 2 1pk8A 30 d.142.1.3 (29) Synapsin I
54 1d9zA 1d9zA 23 c.37.1.19 (23) DNA Repair Protein UVRB
55 1bcpF 1bcpF 9 b.40.2.1 (9) 2.4.2.- Pertussis Toxin 1bcpL 10 b.40.2.1 (10) 2.4.2.- Pertussis Toxin
56 1bcpE 1bcpE 13 b.40.2.1 (13) 2.4.2.- Pertussis Toxin 1bcpK 13 b.40.2.1 (13) 2.4.2.- Pertussis Toxin
57 1u9iA 1e79A 21 c.37.1.11 (17), a.69.1.1 (4) 3.6.1.34 ATP Synthase Alpha Chain Heart Isoform (Bovine Mitochondrial F1-Atpase)
1e79C 22 c.37.1.11 (18), a.69.1.1 (4) 3.6.1.34 ATP Synthase Alpha Chain Heart Isoform (Bovine Mitochondrial F1-Atpase)
1h8hA 23 c.37.1.11 (19), a.69.1.1 (4) 3.6.1.34 ATP Synthase Alpha Chain Heart Isoform 1h8hB 29 c.37.1.11 (18), a.69.1.1 (4) 3.6.1.34 ATP Synthase Alpha Chain Heart Isoform 1h8hC 23 c.37.1.11 (19), a.69.1.1 (4) 3.6.1.34 ATP Synthase Alpha Chain Heart Isoform 1h8hD 7 a.69.1.1 (4) 3.6.1.34 Bovine Mitochondrial F1-Atpase 1h8hF 34 c.37.1.11 (20), a.69.1.1 (11) 3.6.1.34 Bovine Mitochondrial F1-Atpase 1mabA 24 c.37.1.11 (20), a.69.1.1 (4) 3.6.1.34 F1-Atpase Alpha Chain
1tf7A 35 c.37.1.11 (23) Circadian Clock Protein KAIC 1tf7B 35 c.37.1.11 (23) Circadian Clock Protein KAIC 1tf7C 35 c.37.1.11 (24) Circadian Clock Protein KAIC 1tf7D 34 c.37.1.11 (23) Circadian Clock Protein KAIC 1tf7E 36 c.37.1.11 (24) Circadian Clock Protein KAIC 1tf7F 35 c.37.1.11 (24) Circadian Clock Protein KAIC
57 1u9iA 1u9iA 35 Circadian Clock Protein Kaic 1u9iB 35 Circadian Clock Protein Kaic 1u9iC 35 Circadian Clock Protein Kaic 1u9iD 34 Circadian Clock Protein Kaic 1u9iE 36 Circadian Clock Protein Kaic 1u9iF 35 Circadian Clock Protein Kaic
58 2biyA 1atpE 33 d.144.1.7 (33) 2.7.1.37 cAMP-Depedent Protein Kinase (CAPK) 1b38A 30 d.144.1.7 (30) 2.7.1.37 Cell Division Protein Kinase 2
1b39A 32 d.144.1.7 (32) 2.7.1.37 Cell Division Protein Kinase 2 1csn_ 29 d.144.1.7 (29) 2.7.1.- Casein Kinase-1
1e8xA 26 d.144.1.4 (26) 2.7.1.137 Phosphatidylinositol 3-Kinase Catalytic Subunit 1finA 25 d.144.1.7 (25) 2.7.1.- Cyclin-Dependent Kinase 2
1finC 26 d.144.1.7 (26) 2.7.1.- Cyclin-Dependent Kinase 2 1fq1B 27 d.144.1.7 (27) 2.7.1.- Cell Division Protein Kinase 2 1gol_ 22 d.144.1.7 (22) 2.7.1.- Extracellular Regulated Kinase 2 1gy3A 27 d.144.1.7 (27) Cell Division Protein Kinase 2
1gy3C 30 d.144.1.7 (30) Cell Division Protein Kinase 2
1gy3C 30 d.144.1.7 (30) Cell Division Protein Kinase 2