SMTL ID : 3gcm.1

Crystal Structure of E. coli polynucleotide phosphorylase bound to RNA and RNase E

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-3-3-mer

Ligands

8 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 8 residues within 4Å: Chain A: R.93, R.399, H.403, D.486, D.492, K.494, D.508 Ligands: FLC.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:D.508 Hydrogen bonds: A:D.492 Water bridges: A:R.93, A:R.93, A:D.96, A:R.100, A:R.399, A:R.399, A:R.399, A:Q.506, A:Q.506, A:D.508 Salt bridges: A:R.93, A:R.93, A:R.399, A:R.399, A:H.403, A:K.494, A:K.494 FLC.2: 10 residues within 4Å: Chain A: H.403, G.436, S.437, S.438, S.439, H.487, D.492, K.494 Ligands: FLC.1, MG.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.436, A:S.438, A:S.439 Water bridges: A:Y.380, A:R.399, A:R.399, A:H.403 Salt bridges: A:R.399, A:H.403, A:K.494 FLC.6: 9 residues within 4Å: Chain C: L.90, L.94, R.153, D.176, V.178, E.190, S.191, E.192, R.409 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.94, C:E.190 Hydrogen bonds: C:E.190, C:E.192, C:E.192, C:E.192 Water bridges: C:N.125, C:D.127, C:R.153 Salt bridges: C:R.153, C:R.409, C:R.409 FLC.7: 8 residues within 4Å: Chain C: R.93, R.399, H.403, D.486, D.492, K.494, D.508 Ligands: FLC.9 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:D.508 Hydrogen bonds: C:D.508 Water bridges: C:R.93, C:R.93, C:R.93, C:D.96, C:R.399 Salt bridges: C:R.93, C:R.93, C:R.399, C:R.399, C:H.403, C:K.494, C:K.494 FLC.8: 7 residues within 4Å: Chain C: E.192, R.372, D.374, R.405, K.408, R.409, L.412 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:E.192, C:R.405 Water bridges: C:R.372, C:T.375, C:F.376 Salt bridges: C:R.372, C:R.372, C:R.405, C:K.408, C:R.409 FLC.9: 12 residues within 4Å: Chain C: H.403, S.434, G.436, S.437, S.438, S.439, D.486, H.487, D.492, K.494 Ligands: FLC.7, MG.10 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.436, C:S.438, C:S.439, C:S.439 Salt bridges: C:H.403, C:H.487, C:K.494 FLC.12: 8 residues within 4Å: Chain E: R.93, R.399, H.403, D.486, D.492, K.494, D.508 Ligands: FLC.13 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:D.508 Hydrogen bonds: E:D.492 Water bridges: E:R.93, E:R.93, E:Q.506, E:D.508 Salt bridges: E:R.93, E:R.93, E:R.399, E:R.399, E:H.403, E:K.494, E:K.494 FLC.13: 12 residues within 4Å: Chain E: R.399, H.403, G.436, S.437, S.438, S.439, D.486, H.487, D.492, K.494 Ligands: FLC.12, MG.14 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:S.438, E:S.439, E:S.439, E:D.486 Salt bridges: E:R.399, E:H.403, E:H.487, E:K.494

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: S.437, A.465, I.481, D.492 Ligands: FLC.2 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain C: S.437, A.465, I.481, D.492 Ligands: FLC.9 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Chain E: S.437, A.465, I.481, D.492 Ligands: FLC.13 No protein-ligand interaction detected (PLIP)

3 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.4: 3 residues within 4Å: Chain C: F.77 Ligands: 5GP.5, 5GP.11 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A pi-Stacking: C:F.77 pi-Cation interactions: C:F.77 Water bridges: A:D.366, A:D.366 5GP.5: 5 residues within 4Å: Chain C: G.75, D.366 Chain E: F.77, F.78 Ligands: 5GP.4 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C pi-Stacking: E:F.77, E:F.77 Salt bridges: C:D.366 5GP.11: 7 residues within 4Å: Chain A: F.77, F.78 Chain E: G.75, S.76, F.78, D.366 Ligands: 5GP.4 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:D.366 Water bridges: E:S.76, A:F.77 pi-Stacking: A:F.77 pi-Cation interactions: A:F.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nurmohamed, S. et al., Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly. J.Mol.Biol. (2009)

Release Date

2009-06-09

Peptides

Polyribonucleotide nucleotidyltransferase: ACE
Ribonuclease E: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
C

B
D

D
E

F
F

Polyribonucleotide nucleotidyltransferase

Ribonuclease E

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