SMTL ID : 7xif.1 (2 other biounits)

Crystal structure of the aminopropyltransferase, SpeE from hyperthermophilic crenarchaeon, Pyrobaculum calidifontis in complex with 5'-methylthioadenosine (MTA) alone or together with spermidine or thermospermine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-tetramer

Ligands

4 x MTA: 5'-DEOXY-5'-METHYLTHIOADENOSINE(Non-covalent)

MTA.1: 22 residues within 4Å: Chain A: Q.56, L.70, L.72, Q.77, G.108, G.109, G.110, E.111, V.130, D.131, I.132, D.133, V.136, D.163, G.164, D.184, L.185, T.186, I.193, A.194, L.197 Ligands: SPD.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.56, A:G.110, A:I.132, A:D.163, A:G.164, A:T.186, A:I.193 MTA.3: 23 residues within 4Å: Chain B: Q.56, L.70, L.72, Q.77, G.108, G.109, G.110, E.111, V.130, D.131, I.132, D.133, V.136, Q.162, D.163, G.164, D.184, L.185, T.186, I.193, A.194, L.197 Ligands: TER.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.56, B:G.110, B:I.132, B:D.133, B:D.163, B:D.163, B:G.164, B:T.186 MTA.5: 23 residues within 4Å: Chain C: Q.56, L.70, L.72, Q.77, G.108, G.109, G.110, E.111, V.130, D.131, I.132, D.133, V.136, Q.162, D.163, G.164, D.184, L.185, T.186, I.193, A.194, L.197 Ligands: SPD.6 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.56, C:G.110, C:I.132, C:D.133, C:D.163, C:G.164, C:T.186 MTA.7: 23 residues within 4Å: Chain D: Q.56, L.70, L.72, Q.77, G.108, G.109, G.110, E.111, V.130, D.131, I.132, D.133, V.136, Q.162, D.163, G.164, D.184, L.185, T.186, I.193, A.194, L.197 Ligands: SPD.8 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.56, D:G.110, D:I.132, D:G.164, D:T.186, D:I.193

3 x SPD: SPERMIDINE(Non-covalent)

SPD.2: 14 residues within 4Å: Chain A: E.32, P.33, L.34, Y.75, I.76, Q.77, Y.86, D.184, L.185, D.187, Y.189, F.254, Y.256 Ligands: MTA.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.75, A:F.254 Hydrogen bonds: A:P.33, A:Q.77, A:Q.77, A:D.184 SPD.6: 13 residues within 4Å: Chain C: E.32, P.33, I.76, Q.77, Y.86, D.184, L.185, D.187, Y.189, Q.219, F.254, Y.256 Ligands: MTA.5 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.254 Hydrogen bonds: C:P.33, C:Q.77, C:D.184, C:D.187 Water bridges: C:Y.256 SPD.8: 15 residues within 4Å: Chain D: E.32, P.33, L.34, Y.75, I.76, Q.77, Y.86, D.184, L.185, D.187, Y.189, Q.219, F.254, Y.256 Ligands: MTA.7 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.75, D:F.254 Hydrogen bonds: D:P.33, D:I.76, D:D.184

1 x TER: N-(3-AMINO-PROPYL)-N-(5-AMINOPROPYL)-1,4-DIAMINOBUTANE(Non-covalent)

TER.4: 16 residues within 4Å: Chain B: E.32, P.33, Y.75, I.76, Q.77, Y.86, H.87, E.111, D.184, L.185, D.187, Y.189, Q.219, F.254, Y.256 Ligands: MTA.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.86 Hydrogen bonds: B:P.33, B:Q.77, B:Y.86, B:E.111, B:D.184, B:Y.256, B:Y.256 Water bridges: B:E.111, B:D.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukuda, W. et al., Substrate Specificity of an Aminopropyltransferase and the Biosynthesis Pathway of Polyamines in the Hyperthermophilic Crenarchaeon Pyrobaculum calidifontis. Catalysts (2022)

Release Date

2022-06-15

Peptides

Polyamine aminopropyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

C
C

D
H

Polyamine aminopropyltransferase

Related Entries With Identical Sequence