SMTL ID : 7xii.1

Crystal structure of the aminopropyltransferase, SpeE from hyperthermophilic crenarchaeon, Pyrobaculum calidifontis in complex with 5'-methylthioadenosine (MTA) & aminopropylagmatine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

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

MTA.1: 23 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, Q.162, D.163, G.164, D.184, L.185, T.186, I.193, A.194, L.197 Ligands: AG3.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.56, A:G.108, A:G.110, A:I.132, A:G.164, A:T.186, A:I.193 MTA.4: 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: AG3.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.56, B:G.108, B:G.110, B:I.132, B:G.164, B:T.186, B:I.193 MTA.6: 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: AG3.7 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Q.56, C:G.108, C:G.110, C:I.132, C:D.163, C:G.164, C:T.186, C:I.193 MTA.8: 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: AG3.9 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.56, D:G.108, D:G.110, D:I.132, D:D.163, D:D.163, D:G.164, D:T.186

4 x AG3: 1-{4-[(3-aminopropyl)amino]butyl}guanidine(Non-covalent)

AG3.2: 15 residues within 4Å: Chain A: E.32, 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.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.86, A:F.254, A:F.254 Hydrogen bonds: A:I.76, A:E.111, A:L.185, A:Y.189 Water bridges: A:D.187 Salt bridges: A:E.32, A:D.187 pi-Cation interactions: A:F.254 AG3.5: 15 residues within 4Å: Chain B: E.32, 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.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.86, B:F.254 Hydrogen bonds: B:I.76, B:Q.77, B:E.111, B:L.185, B:Y.189, B:Y.256 Salt bridges: B:E.32, B:D.187 pi-Cation interactions: B:F.254 AG3.7: 15 residues within 4Å: Chain C: E.32, 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.6 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.86, C:F.254, C:F.254 Hydrogen bonds: C:I.76, C:Q.77, C:E.111, C:L.185, C:Y.189, C:Y.189, C:Y.256 Water bridges: C:T.114 Salt bridges: C:E.32, C:D.187 pi-Cation interactions: C:F.254 AG3.9: 15 residues within 4Å: Chain D: E.32, 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.8 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:Q.77, D:Y.86, D:F.254, D:F.254 Hydrogen bonds: D:I.76, D:Q.77, D:D.184, D:Y.189, D:Y.189, D:Y.256 Water bridges: D:T.114 Salt bridges: D:E.32, D:D.187 pi-Cation interactions: D:F.254

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 7 residues within 4Å: Chain A: P.99, Y.267, A.271, L.272, T.273, E.276, R.280 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.280, A:R.280 Salt bridges: A:E.276, A:E.276, A:R.280

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
B

C
C

D
D

Polyamine aminopropyltransferase

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