1. Register problem Green: MocoBD_1C; Yellow: MocoBD_2C Register 1 Register 2 90 residues aligned with RMSD 2.58 A92 residues aligned with RMSD 2.61 A

2. Structural features for choosing the registers (1N & 2N) DmpA_1OAT_1 OAT_2DmpA_2 MocoBD_1NMocoBD_2N MocoBD_2CMocoBD_1C Green: MocoBD_1N Yellow: MocoBD_2N The loop between helix A and strand d, including a one-turn helix, aligns closely. This feature (marked with @) fixes the alignment between 1N and 2N. 1N 2N

3. Structural features for choosing the registers (1C & 2C) DmpA_1OAT_1 OAT_2DmpA_2 MocoBD_1NMocoBD_2N MocoBD_2CMocoBD_1C Orange: MocoBD_2C; Others: MocoBD_1C in different structures 1C and 2C both have a highly conserved Asp at the end of strand c (marked with #) that uses its side chain O  to hydrogen bond with the backbone NH group of the residue two positions after it. 1C 2C

4. Structural features for choosing the registers ( 1N & 2C ) DmpA_1OAT_1 OAT_2DmpA_2 MocoBD_1NMocoBD_2N MocoBD_2CMocoBD_1C Green: MocoBD_1N; Orange: MocoBD_2C 1N 2C Both 1N and 2C have a largely conserved Pro at the beginning of helix A (marked with &) that superimpose closely. This feature fixes the register of 1N and 2C. Thus, the four units in MocoBD can be aligned.

5. DmpA and OAT can be aligned unambiguously DmpA_1OAT_1 OAT_2DmpA_2 MocoBD_1NMocoBD_2N MocoBD_2CMocoBD_1C Green: DmpA; Yellow: OAT domain 1 DmpA and OAT can be aligned unambiguously using the nucleophile as reference. Thus the alignment between DmpA_1 and OAT_1 as well as the alignment between DmpA_2 and OAT_2 are fixed.

6. Structural features for choosing the registers (DmpA_1 & DmpA_2) DmpA_1OAT_1 OAT_2DmpA_2 MocoBD_1NMocoBD_2N MocoBD_2CMocoBD_1C Red: DmpA_1; Green: DmpA_2; Light green: OAT_2 DmpA_1 DmpA_2 OAT_2 DmpA_1 and DmpA_2 both have a conserved T at the end of strand c (marked with *) that uses its side chain O  to hydrogen bond with a backbone carbonyl group on strand b. This T is also observed in OAT_2.

7. 1N 2N OAT_1 Structural features for choosing the registers (1N, 2N & OAT_1) DmpA_1OAT_1 OAT_2DmpA_2 MocoBD_1NMocoBD_2N MocoBD_2CMocoBD_1C Green: 1N; Yellow: 2N; Red: OAT_1 The feature used for choosing the register between 1N and 2N (the loop connecting helix A and strand d) has the same conformation in OAT_1. So the alignment between OAT_1, 1N, and 2N is fixed. This means that all the domains can be aligned together now.