SMTL ID : 4lno.1

B. subtilis glutamine synthetase structures reveal large active site conformational changes and basis for isoenzyme specific regulation: form two of GS-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-12-mer

Ligands

24 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: E.133, H.186, E.188, E.195 Ligands: GLN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.133, A:E.188, A:E.195 MG.2: 5 residues within 4Å: Chain A: E.131, H.244, E.332 Chain B: E.64 Ligands: GLN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.131, A:H.244, A:E.332 MG.4: 4 residues within 4Å: Chain B: E.133, E.188, E.195 Ligands: GLN.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.133, B:E.188, B:E.195, H2O.8 MG.5: 4 residues within 4Å: Chain B: E.131, H.244, E.332 Chain C: E.64 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.131, B:H.244, B:E.332 MG.8: 4 residues within 4Å: Chain C: E.131, H.244, E.332 Chain D: E.64 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.131, C:H.244 MG.9: 4 residues within 4Å: Chain C: E.133, E.188, E.195 Ligands: GLN.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.133, C:E.188, C:E.195 MG.10: 4 residues within 4Å: Chain D: E.133, E.188, E.195 Ligands: GLN.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.133, D:E.188, D:E.195 MG.11: 4 residues within 4Å: Chain D: E.131, H.244, E.332 Chain E: E.64 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.131, D:H.244, D:E.332, H2O.18 MG.13: 4 residues within 4Å: Chain E: E.131, H.244, E.332 Chain F: E.64 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.131, E:H.244, E:E.332, H2O.20, H2O.24 MG.14: 4 residues within 4Å: Chain E: E.133, E.188, E.195 Ligands: GLN.15 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.133, E:E.188, E:E.195 MG.16: 4 residues within 4Å: Chain A: E.64 Chain F: E.131, H.244, E.332 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.131, F:H.244, F:E.332 MG.17: 4 residues within 4Å: Chain F: E.133, E.188, E.195 Ligands: GLN.18 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.133, F:E.188, F:E.195 MG.19: 5 residues within 4Å: Chain G: E.133, H.186, E.188, E.195 Ligands: GLN.21 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.133, G:E.188, G:E.195 MG.20: 5 residues within 4Å: Chain G: E.131, H.244, E.332 Chain H: E.64 Ligands: GLN.21 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.131, G:H.244, G:E.332 MG.22: 4 residues within 4Å: Chain H: E.133, E.188, E.195 Ligands: GLN.24 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.133, H:E.188, H:E.195, H2O.36 MG.23: 4 residues within 4Å: Chain H: E.131, H.244, E.332 Chain I: E.64 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.131, H:H.244, H:E.332 MG.26: 4 residues within 4Å: Chain I: E.131, H.244, E.332 Chain J: E.64 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:E.131, I:H.244 MG.27: 4 residues within 4Å: Chain I: E.133, E.188, E.195 Ligands: GLN.25 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.133, I:E.188, I:E.195 MG.28: 4 residues within 4Å: Chain J: E.133, E.188, E.195 Ligands: GLN.30 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.133, J:E.188, J:E.195 MG.29: 4 residues within 4Å: Chain J: E.131, H.244, E.332 Chain K: E.64 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.131, J:H.244, J:E.332, H2O.46 MG.31: 4 residues within 4Å: Chain K: E.131, H.244, E.332 Chain L: E.64 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.131, K:H.244, K:E.332, H2O.47, H2O.51 MG.32: 4 residues within 4Å: Chain K: E.133, E.188, E.195 Ligands: GLN.33 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.133, K:E.188, K:E.195 MG.34: 4 residues within 4Å: Chain G: E.64 Chain L: E.131, H.244, E.332 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.131, L:H.244, L:E.332 MG.35: 4 residues within 4Å: Chain L: E.133, E.188, E.195 Ligands: GLN.36 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.133, L:E.188, L:E.195

12 x GLN: GLUTAMINE(Non-covalent)

GLN.3: 11 residues within 4Å: Chain A: E.133, Y.155, E.188, Q.193, N.239, G.240, H.244, R.297, E.303 Ligands: MG.1, MG.2 6 PLIP interactions: 6 interactions with chain A, Hydrogen bonds: A:Y.155, A:N.239, A:R.297 Water bridges: A:E.133, A:G.240, A:H.244 GLN.6: 12 residues within 4Å: Chain B: E.133, Y.155, E.188, N.239, G.240, G.242, H.244, R.297, E.303, A.304, R.334 Ligands: MG.4 7 PLIP interactions: 6 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:E.303 Hydrogen bonds: B:Y.155, B:G.240, B:R.297, B:E.303, Q.6 Water bridges: B:V.189 GLN.7: 11 residues within 4Å: Chain C: E.133, Y.155, E.188, Q.193, G.240, G.242, H.244, R.297, E.303, A.304 Ligands: MG.9 7 PLIP interactions: 7 interactions with chain C, Hydrogen bonds: C:E.133, C:Y.155, C:G.240 Water bridges: C:E.303, C:R.334 Salt bridges: C:H.244, C:R.297 GLN.12: 12 residues within 4Å: Chain D: E.133, Y.155, E.188, G.240, G.242, H.244, R.297, Y.302, E.303, A.304, R.334 Ligands: MG.10 8 PLIP interactions: 7 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:E.303 Hydrogen bonds: D:G.240, D:E.303, Q.12 Water bridges: D:V.189, D:R.334 Salt bridges: D:H.244, D:R.297 GLN.15: 11 residues within 4Å: Chain E: E.133, Y.155, E.188, Q.193, N.239, G.240, H.244, R.297, E.303 Chain F: R.61 Ligands: MG.14 10 PLIP interactions: 7 interactions with chain E, 2 interactions with chain F, 1 Ligand-Ligand interactions Hydrogen bonds: E:Y.155, E:Q.193, E:G.240, E:G.240, F:R.61 Water bridges: E:R.334, F:D.52, Q.15 Salt bridges: E:H.244, E:R.297 GLN.18: 11 residues within 4Å: Chain F: E.133, Y.155, E.188, Q.193, G.240, H.244, R.297, Y.302, E.303, A.304 Ligands: MG.17 5 PLIP interactions: 5 interactions with chain F, Hydrophobic interactions: F:E.303 Hydrogen bonds: F:G.240, F:G.240 Salt bridges: F:H.244, F:R.297 GLN.21: 11 residues within 4Å: Chain G: E.133, Y.155, E.188, Q.193, N.239, G.240, H.244, R.297, E.303 Ligands: MG.19, MG.20 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:N.239, G:R.297 Water bridges: G:E.133, G:E.133, G:G.240 GLN.24: 12 residues within 4Å: Chain H: E.133, Y.155, E.188, N.239, G.240, G.242, H.244, R.297, E.303, A.304, R.334 Ligands: MG.22 6 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain H Hydrogen bonds: Q.24, H:G.240, H:R.297, H:E.303 Hydrophobic interactions: H:E.303 Water bridges: H:V.189 GLN.25: 11 residues within 4Å: Chain I: E.133, Y.155, E.188, Q.193, G.240, G.242, H.244, R.297, E.303, A.304 Ligands: MG.27 5 PLIP interactions: 5 interactions with chain I, Hydrogen bonds: I:E.133, I:G.240 Water bridges: I:R.334 Salt bridges: I:H.244, I:R.297 GLN.30: 12 residues within 4Å: Chain J: E.133, Y.155, E.188, G.240, G.242, H.244, R.297, Y.302, E.303, A.304, R.334 Ligands: MG.28 9 PLIP interactions: 8 interactions with chain J, 1 Ligand-Ligand interactions Hydrophobic interactions: J:E.303 Hydrogen bonds: J:Y.155, J:G.240, J:E.303, Q.30 Water bridges: J:V.189, J:R.334 Salt bridges: J:H.244, J:R.297 GLN.33: 11 residues within 4Å: Chain K: E.133, Y.155, E.188, Q.193, N.239, G.240, H.244, R.297, E.303 Chain L: R.61 Ligands: MG.32 10 PLIP interactions: 8 interactions with chain K, 1 Ligand-Ligand interactions, 1 interactions with chain L Hydrogen bonds: K:Y.155, K:Y.155, K:Q.193, K:G.240, K:G.240, L:R.61 Water bridges: K:R.334, Q.33 Salt bridges: K:H.244, K:R.297 GLN.36: 11 residues within 4Å: Chain L: E.133, Y.155, E.188, Q.193, G.240, H.244, R.297, Y.302, E.303, A.304 Ligands: MG.35 6 PLIP interactions: 6 interactions with chain L, Hydrophobic interactions: L:E.303 Hydrogen bonds: L:Y.155, L:G.240, L:G.240 Salt bridges: L:H.244, L:R.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murray, D.S. et al., Structures of the Bacillus subtilis Glutamine Synthetase Dodecamer Reveal Large Intersubunit Catalytic Conformational Changes Linked to a Unique Feedback Inhibition Mechanism. J.Biol.Chem. (2013)

Release Date

2013-11-13

Peptides

Glutamine synthetase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

Glutamine synthetase

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