SMTL ID : 6n9a.1

Crystal Structure of Thermotoga maritima threonylcarbamoyladenosine biosynthesis complex TsaB2D2E2 bound to ATP and carboxy-AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 3 residues within 4Å: Chain A: D.51, E.52, D.54 No protein-ligand interaction detected (PLIP) PGE.8: 3 residues within 4Å: Chain D: D.51, E.52, D.54 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.54

2 x AE3: 2-(2-ETHOXYETHOXY)ETHANOL(Non-covalent)

AE3.2: 4 residues within 4Å: Chain A: E.52 Chain D: I.30, K.36 Ligands: AE3.9 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.30 AE3.9: 4 residues within 4Å: Chain A: I.30, K.36 Chain D: E.52 Ligands: AE3.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.30

2 x KG4: 5'-O-[(R)-(carboxyoxy)(hydroxy)phosphoryl]adenosine(Non-covalent)

KG4.3: 17 residues within 4Å: Chain B: S.137, G.138, G.139, G.164, F.167, D.168, G.180, G.181, P.182, D.185, G.266, G.267, V.268, A.270, N.271, T.298 Chain C: F.65 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.138, B:G.139, B:D.168, B:G.180, B:G.181, B:D.185, B:G.267, B:N.271 Water bridges: B:S.137, B:S.137 pi-Stacking: B:F.167 KG4.10: 17 residues within 4Å: Chain E: S.137, G.138, G.139, G.164, F.167, D.168, G.180, G.181, P.182, D.185, G.266, G.267, V.268, A.270, N.271, T.298 Chain F: F.65 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.138, E:G.139, E:D.168, E:G.180, E:G.181, E:D.185, E:D.185, E:G.267, E:N.271 Water bridges: E:S.137, E:S.137 pi-Stacking: E:F.167

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain B: H.112, H.116, H.140, D.299 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.112, B:H.116, B:H.140, B:D.299, H2O.2, H2O.3 ZN.11: 4 residues within 4Å: Chain E: H.112, H.116, H.140, D.299 6 PLIP interactions: 4 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.112, E:H.116, E:H.140, E:D.299, H2O.8, H2O.10

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 4 residues within 4Å: Chain B: F.251, R.255, W.285, Y.287 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.255, B:Y.287, B:Y.287 Salt bridges: B:R.255, B:R.255 pi-Stacking: B:W.285, B:W.285, B:W.285, B:W.285 pi-Cation interactions: B:R.255, B:R.255 ADP.12: 4 residues within 4Å: Chain E: F.251, R.255, W.285, Y.287 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:R.255, E:Y.287 Salt bridges: E:R.255, E:R.255 pi-Stacking: E:W.285, E:W.285, E:W.285, E:W.285 pi-Cation interactions: E:R.255, E:R.255

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.6: 25 residues within 4Å: Chain B: K.169, A.213, G.214, K.216, T.217, Y.221 Chain C: L.10, T.11, E.12, L.15, N.37, L.38, G.39, A.40, G.41, K.42, T.43, T.44, E.109, W.110, E.132, S.133, H.134, R.135 Ligands: MG.7 27 PLIP interactions: 20 interactions with chain C, 7 interactions with chain B Hydrogen bonds: C:E.12, C:G.39, C:A.40, C:G.41, C:G.41, C:K.42, C:T.43, C:T.44, C:T.44, C:S.133, B:A.213 Water bridges: C:T.43, C:T.43, C:T.43, C:T.43, C:D.81, C:W.110, B:K.169, B:K.169 Salt bridges: C:K.42, C:K.42, B:K.169, B:K.216, B:K.216, B:K.216 pi-Cation interactions: C:R.135, C:R.135 ATP.13: 25 residues within 4Å: Chain E: K.169, A.213, G.214, K.216, T.217, Y.221 Chain F: L.10, T.11, E.12, L.15, N.37, L.38, G.39, A.40, G.41, K.42, T.43, T.44, E.109, W.110, E.132, S.133, H.134, R.135 Ligands: MG.14 27 PLIP interactions: 16 interactions with chain F, 11 interactions with chain E Hydrogen bonds: F:E.12, F:G.39, F:A.40, F:G.41, F:G.41, F:K.42, F:T.43, F:T.43, F:T.44, F:T.44, F:S.133, E:A.213, E:T.217 Water bridges: F:W.110, E:K.169, E:K.169, E:K.169, E:K.169, E:K.169 Salt bridges: F:K.42, F:K.42, E:K.169, E:K.216, E:K.216, E:K.216 pi-Cation interactions: F:R.135, F:R.135

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain C: T.43, E.109 Ligands: ATP.6 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.43, C:E.109, H2O.5, H2O.5 MG.14: 3 residues within 4Å: Chain F: T.43, E.109 Ligands: ATP.13 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:T.43, F:E.109, H2O.11, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luthra, A. et al., Conformational communication mediates the reset step in t6A biosynthesis. Nucleic Acids Res. (2019)

Release Date

2019-05-22

Peptides

tRNA threonylcarbamoyladenosine biosynthesis protein TsaB: AD
tRNA N6-adenosine threonylcarbamoyltransferase: BE
tRNA threonylcarbamoyladenosine biosynthesis protein TsaE: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
B

B
D

E
D

C
E

F
E

tRNA threonylcarbamoyladenosine biosynthesis protein TsaB

tRNA N6-adenosine threonylcarbamoyltransferase

tRNA threonylcarbamoyladenosine biosynthesis protein TsaE