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. 2018 Nov 12;28(2):344–364. doi: 10.1002/pro.3527

Table 3.

Amino Acid Sets that Form Aromatic Clusters Near the Active Site

N SCOP Family #/
SCOP family name 		PDB ID
Resolution 		XoxyII XoxyII‐4 W/Y/F Xnuc‐1 Snuc SC/XozII ± 1 – O/HoxyII‐2
A 2. Carboxylesterase 3WJ2_A23
1.61 Å 		G85 Y81 Y95 D155 S156 OH/Y115‐O/H83; 2.6
1 1. Acetylcholinesterase‐like 1QE3_A75
1.50 Å 		G106 W102 Y118 E188 S189 OH/Y136‐O/H104; 2.7
2 2. Carboxylesterase 1LZL_A76
1.30 Å 		G88 W84 S98 Q159 S160 OH/Y118‐O/H86; 2.7
3 3. Mycobacterial antigens 1DQZ_A47
1.50 Å 		L40 L36 W49 L123 S124 O/G71‐OH/Y77; 4.0
CE1/Y77‐O/D38; 3.6
4 4. Hypothetical protein TT1662 1UFO_A77
1.60 Å 		L33 A29 I40 G112 S113 CB/A59‐π/F88; 3.4
CE2/F88‐O/H31; 3.5
5 5. PepX catalytic domain‐like 3PUI_A24
1.53 Å 		OH/Y44 V40 W52 V116 S117 ‐
6 6. Prolyl oligopeptidase, C‐terminal domain 1H2W_A25
1.39 Å 		OH/Y473 Y471 I480 G553 S554 ‐
7 7. DPP4 catalytic domain‐like 1ORV_A26
1.80 Å 		OH/Y547 E545 K554 W629 S630 ‐
8 8. Serine carboxypeptidase‐like 3SC2_A48
2.20 Å 		G53 W49 S58 E145 S146 O/S95‐OH/Y151; 4.4
CE2/Y151‐O/N51; 3.1
9 9. Gastric lipase 1HLG_A46
3.00 Å 		L67 L63 W74 H152 S153 OG/S99‐OE1/Q64; 3.7
NE2/Q64‐O/H65; 3.3
10 10. Proline iminopeptidase‐like 1MTZ_A78
1.80 Å 		G37 T33 L45 S104 S105 OE1/Q63‐O/H35; 3.0
11 11. Acetyl xylan esterase‐like 1L7A_A79
1.50 Å 		Y91 K87 E98 G180 S181 CG2/V117‐NE2/Q182;3.9
NE2/Q182‐O/H89; 2.8
12 12. Haloalkane dehalogenase 1MJ5_A80
0.95 Å 		N38 F34 W45 H107 D108 CD1/L63‐O/H36; 3.8
13 13. Dienelactone hydrolase 1ZI9_A27
1.50 Å 		I37 I33 M44 Y122 S123 CD1/L63‐CD1/L128; 3.7
CD1/L128‐O/Q35; 5.4
14 14. Carbon–carbon bond hydrolase 2OG1_A81
1.60 Å 		G42 M38 Y52 N111 S112 CB/S71‐CE/M113; 4.0
CE/M113‐O/H40; 4.0
15 15. Biotin biosynthesis protein BioH 4ETW_A82
2.05 Å 		W22 L18 W29 W81 A82a CD1/L47‐O/H20; 3.5
16 16. Aclacinomycin methylesterase RdmC 1Q0R_A28
1.45 Å 		G32 L28 W39 L101 S102 CE1/H59‐O/M30; 2.9
17 17. Carboxylesterase/lipase 4DIU_A83
2.00 Å 		F24 L20 V31 L92 S93 OH/Y50‐O/H22; 3.0
18 18. Epoxide hydrolase 1QO7_A84
1.80 Å 		W117 L113 F124 G191 D192 CD1/L149‐O/H115; 3.6
19 19. Haloperoxidase 1BRT_A85
1.50 Å 		F32 L28 W39 F97 S98 CD/R58‐O/H30; 3.2
20 20. Thioesterases 1EI9_A86
2.25 Å 		M41 I37 M51 F114 S115 CD1/I72‐CZ2/W38; 4.3
CD1/W38‐O/H39; 3.2
21 21. Carboxylesterase/
thioesterase 1 		1FJ2_A87
1.50 Å 		L25 F21 W32 F113 S114 CB/A51‐π/W67; 3.5
NE1/W67‐O/H23; 2.7
22 22. Ccg1/TafII250‐interacting factor B (Cib) 1IMJ_A88
2.20 Å 		I41 L37 W48 P110 S111 CD2/L69‐O/H39; 4.4
23 23. A novel bacterial esterase 1QLW_A89
1.09 Å 		C71 L67 W78 H205 S206 NE2/Q104‐O/H69; 3.0
24 24. Lipase 1JFR_A30
1.90 Å 		F63 I59 I70 H130 S131 OG1/T89‐NH1/R99; 3.9
NH1/R99‐O/P61; 2.8
25 25. Fungal lipases 1TCA_A31
1.55 Å 		T40 L36 F48 W104 S105 CG/P68‐SD/M72; 3.7
CE/M72‐O/P38; 3.2
26 26. Bacterial lipase 1ISP_A90
1.30 Å 		I12 M8 F19 H76 S77 CE2/F41‐O/H10; 3.7
27 27. Pancreatic lipase, N‐terminal domain 1BU8_A91
1.80 Å 		F77 I73 W85 H151 S152 NE1/W106‐O/H75; 3.0
28 28. Hydroxynitrile lyase‐like 3C6X_A92
1.05 Å 		I12 L8 W19 E79 S80 CD1/L38‐O/H10; 3.9
29 29. Thioesterase domain of polypeptide, polyketide and fatty acid synthases 1JMK_C32
1.71 Å 		V27 A23 Y34 Y79 S80 CB/F51‐π/F155; 4.3
CE1/F155‐O/P25; 3.3
30 30. Cutinase‐like 1BS9_A29
1.10 Å 		T13 G9 S22 Y89 S90 OH/Y43‐O/R11; 2.7
31 31. YdeN‐like 1UXO_A93
1.80 Å 		Y11 I7 F20 H70 S71 CG/M39‐π/W50; 3.5
CZ3/W50‐O/H9; 3.5
32 32. Putative serine hydrolase Ydr428c 1VKH_A94
1.85 Å 		G38 Y34 F50 H109 S110 OH/Y73‐O/H36; 2.7
33 33. Acylamino‐acid‐releasing enzyme, C‐terminal domain 1VE6_A95
2.10 Å 		G369 L365 F381 Y444 S445 OH/Y397‐O/H367; 2.8
34 34. Hypothetical esterase YJL068C 1PV1_A96
2.30 Å 		L58 Y54 A65 H160 S161 CG2/T87‐O/S56; 3.7
35 35. Hypothetical protein VC1974 1R3D_A97
1.90 Å 		L24 L20 W31 Y90 S91 CD1/L50‐O/H22; 3.5
36 36. Atu1826‐like 2I3D_A98
1.50 Å 		H34 I30 V46 Y107 S108 CE2/F65‐O/H32; 3.4
37 37. PHB depolymerase‐like 2D80_A35
1.70 Å 		C250 A246 F261 L38 S39 CB/A283‐π/W305; 4.0
NE1/W305‐O/H248; 2.9
38 38. IroE‐like 2GZS_A11
1.40 Å 		NH1/R130 M88 V94 H188 S189 ‐
40 39. O‐acetyltransferase 2B61_A99
1.65 Å 		L49 I45 W65 G142 S143 CG1/V87‐OE1/Q148; 3.4
NE2/Q148‐O/H47; 2.9
41 40. 2,6‐dihydropseudo‐
oxynicotine hydrolase‐like 		2JBW_A49
2.10 Å 		L147 M143 S154 R216 S217 N/G173‐OE1/Q176; 2.8
NE2/Q176‐O/G145; 3.0

The plane of nucleophile and oxyanion zones in ABH families is sandwiched between aromatic residues. Three specific positions (Columns XoxyII‐4, W/Y/F, Xnuc‐1), which lie close to the catalytic nucleophile (Column Snuc), and the Oxyanion I residue (Column XoxyII), are frequently occupied by aromatic amino acids. An aromatic pair is often formed between the residue side chain (SC) that precedes or follows the position “Oxyanion zone II” and the conserved histidine of the oxyanion zone (Column SC/XozII ± 1–O/HoxyII‐2). The “‐” sign designates exceptions, where the respective bond is not formed, or where there is no residue at that position that can interact with other residues of the aromatic cluster.

a

As is shown in Table 1, in biotin biosynthesis protein BioH (SCOP Family 15), the nucleophile is serine,100, 101 and not alanine, as in the mutant with the PDB ID: 4ETW.82 This, however, does not interfere with the formation of the aromatic cluster.