SMTL ID : 8tg4.1

tRNA 2'-phosphotransferase (Tpt1) from Aeropyrum pernix in complex with ADP-ribose-2"-phosphate and 2'-OH RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

monomer

Ligands

1 x U- G- U- A: RNA (5'-R(*UP*GP*UP*A)-3')(Non-covalent)

U-G-U-A.1: 15 residues within 4Å: Chain A: R.22, V.23, S.26, K.27, A.30, G.31, R.34, H.35, H.36, R.83, Y.84, R.135, R.136, R.154 Ligands: 9SO.4 Protein-ligand interaction information (PLIP) not available

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 4 residues within 4Å: Chain A: P.110, R.170, K.175, V.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.170, A:R.170, A:V.176

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: H.36, P.37, G.38, R.39 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.38, A:R.39, A:R.39, A:R.39

1 x 9SO: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3R,4R,5R)-3,5-dihydroxy-4-(phosphonooxy)oxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)(Non-covalent)

9SO.4: 20 residues within 4Å: Chain A: R.34, K.81, R.83, Y.95, G.96, H.116, T.118, A.122, L.125, I.126, G.130, I.131, M.132, R.136, H.140, T.151, R.154, H.155 Ligands: U-G-U-A.1, K.8 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.130, A:M.132, A:H.155 Water bridges: A:K.81, A:H.116, A:T.119, A:R.136, A:T.151, A:T.151, A:R.154, A:H.155 Salt bridges: A:R.34, A:K.81, A:R.83, A:H.116, A:R.136, A:R.136, A:R.154, A:R.154, A:H.155, A:H.155

4 x K: POTASSIUM ION(Non-covalent)

K.5: 4 residues within 4Å: Chain A: R.43, A.50, R.51, E.54 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:R.43, A:E.54 K.6: 5 residues within 4Å: Chain A: K.138, K.175, E.177, T.185, V.186 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.177, A:T.185, A:T.185 K.7: 5 residues within 4Å: Chain A: R.34, R.83, A.93, R.94, Y.95 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:R.83 K.8: 4 residues within 4Å: Chain A: K.138, V.139, H.140 Ligands: 9SO.4 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 6 residues within 4Å: Chain A: G.96, H.97, R.136, L.137, K.138, H.140 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: R.87, N.88 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jacewicz, A. et al., Structural basis for Tpt1-catalyzed 2'-PO 4 transfer from RNA and NADP(H) to NAD. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-11-08

Peptides

Probable RNA 2'-phosphotransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Probable RNA 2'-phosphotransferase

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