SMTL ID : 4lnk.1

B. subtilis glutamine synthetase structures reveal large active site conformational changes and basis for isoenzyme specific regulation: structure of GS-glutamate-AMPPCP complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.87 Å

Oligo State

homo-12-mer

Ligands

12 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 13 residues within 4Å: Chain A: E.133, Y.155, E.188, V.189, N.239, G.240, G.242, H.244, R.297, E.303, P.305, R.334 Ligands: MG.4 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:G.240, A:R.297, A:E.303, A:E.303, E.1 Salt bridges: A:H.244, A:R.334 GLU.7: 11 residues within 4Å: Chain B: E.133, E.188, N.239, G.240, H.244, R.297, Y.302, E.303, R.334 Chain C: R.61 Ligands: MG.9 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:E.303 Hydrogen bonds: B:E.133, B:G.240, B:G.242, B:R.297 Salt bridges: B:H.244, B:R.334, C:R.61 GLU.11: 13 residues within 4Å: Chain C: E.133, Y.155, E.188, V.189, Q.193, N.239, G.240, G.242, H.244, R.297, E.303, A.304 Ligands: MG.13 12 PLIP interactions: 10 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:V.189 Hydrogen bonds: C:E.133, C:E.188, C:Q.193, C:N.239, C:G.242, C:G.242, E.11, E.11 Water bridges: C:G.240 Salt bridges: C:H.244, C:R.297 GLU.15: 13 residues within 4Å: Chain D: E.133, Y.155, E.188, V.189, N.239, G.240, G.242, H.244, R.297, Y.302, E.303, A.304 Ligands: MG.17 9 PLIP interactions: 6 interactions with chain D, 3 Ligand-Ligand interactions Hydrophobic interactions: D:E.303 Hydrogen bonds: D:G.240, D:G.242, E.15, E.15, E.15 Salt bridges: D:H.244, D:R.297, D:R.334 GLU.19: 12 residues within 4Å: Chain E: E.133, E.188, N.239, G.240, G.242, H.244, R.297, E.303, A.304, P.305, R.334 Ligands: MG.22 8 PLIP interactions: 8 interactions with chain E, Hydrogen bonds: E:N.239, E:G.240, E:E.303, E:E.303 Salt bridges: E:H.244, E:H.244, E:R.297, E:R.334 GLU.24: 13 residues within 4Å: Chain A: R.61 Chain F: E.133, Y.155, E.188, V.189, N.239, G.240, H.244, R.297, E.303, A.304, R.334 Ligands: MG.27 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:E.303 Hydrogen bonds: F:E.133, F:G.240, F:R.297 Salt bridges: A:R.61 GLU.28: 13 residues within 4Å: Chain G: E.133, Y.155, E.188, V.189, N.239, G.240, G.242, H.244, R.297, E.303, P.305, R.334 Ligands: MG.31 8 PLIP interactions: 7 interactions with chain G, 1 Ligand-Ligand interactions Hydrogen bonds: G:Y.155, G:G.240, G:R.297, G:E.303, G:E.303, E.28 Salt bridges: G:H.244, G:R.334 GLU.34: 11 residues within 4Å: Chain H: E.133, E.188, N.239, G.240, H.244, R.297, Y.302, E.303, R.334 Chain I: R.61 Ligands: MG.36 9 PLIP interactions: 1 interactions with chain I, 8 interactions with chain H, Salt bridges: I:R.61, H:H.244, H:R.334 Hydrophobic interactions: H:E.303 Hydrogen bonds: H:E.133, H:G.240, H:G.242, H:R.297, H:E.303 GLU.38: 13 residues within 4Å: Chain I: E.133, Y.155, E.188, V.189, Q.193, N.239, G.240, G.242, H.244, R.297, E.303, A.304 Ligands: MG.40 12 PLIP interactions: 10 interactions with chain I, 2 Ligand-Ligand interactions Hydrophobic interactions: I:V.189 Hydrogen bonds: I:E.133, I:E.188, I:Q.193, I:N.239, I:G.242, I:G.242, E.38, E.38 Water bridges: I:G.240 Salt bridges: I:H.244, I:R.297 GLU.42: 13 residues within 4Å: Chain J: E.133, Y.155, E.188, V.189, N.239, G.240, G.242, H.244, R.297, Y.302, E.303, A.304 Ligands: MG.44 8 PLIP interactions: 7 interactions with chain J, 1 Ligand-Ligand interactions Hydrophobic interactions: J:E.303 Hydrogen bonds: J:Y.155, J:G.240, J:G.242, E.42 Salt bridges: J:H.244, J:R.297, J:R.334 GLU.46: 12 residues within 4Å: Chain K: E.133, E.188, N.239, G.240, G.242, H.244, R.297, E.303, A.304, P.305, R.334 Ligands: MG.49 7 PLIP interactions: 7 interactions with chain K, Hydrogen bonds: K:N.239, K:G.240, K:E.303 Salt bridges: K:H.244, K:H.244, K:R.297, K:R.334 GLU.51: 13 residues within 4Å: Chain G: R.61 Chain L: E.133, Y.155, E.188, V.189, N.239, G.240, H.244, R.297, E.303, A.304, R.334 Ligands: MG.54 5 PLIP interactions: 4 interactions with chain L, 1 interactions with chain G, Hydrophobic interactions: L:E.303 Hydrogen bonds: L:E.133, L:G.240, L:R.297 Salt bridges: G:R.61

12 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 14 residues within 4Å: Chain A: N.127, G.129, F.198, K.199, Y.200, N.246, S.248, F.250, S.324, I.327, S.328, R.330 Chain B: K.43, M.50 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:F.198, A:Y.200, A:S.248, A:S.248, A:N.255, A:S.324, A:S.328, A:R.330, A:R.330 Salt bridges: A:R.330, B:K.43, B:K.43 pi-Cation interactions: A:R.330 ADP.8: 16 residues within 4Å: Chain B: N.127, G.129, E.183, F.198, K.199, Y.200, N.246, S.248, N.255, S.324, I.327, S.328, T.329, R.330 Chain C: K.43, M.50 13 PLIP interactions: 3 interactions with chain C, 10 interactions with chain B Hydrogen bonds: C:K.48, B:G.129, B:F.198, B:S.248, B:S.248, B:N.255, B:S.324, B:S.328 Salt bridges: C:K.43, C:K.43, B:R.330, B:R.330 pi-Stacking: B:Y.200 ADP.12: 14 residues within 4Å: Chain C: N.127, G.129, F.198, Y.200, N.246, L.247, S.248, N.255, S.324, I.327, S.328, R.330 Chain D: K.43, M.50 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.129, C:F.198, C:N.246, C:S.248, C:N.255, C:S.324, C:S.324, C:I.327, C:S.328, D:Y.68 Salt bridges: C:R.330, C:R.330, D:K.43 pi-Stacking: C:Y.200 ADP.16: 14 residues within 4Å: Chain D: G.129, E.183, D.197, F.198, K.199, Y.200, N.246, S.248, S.324, I.327, S.328, R.330 Chain E: K.43, M.50 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:F.198, D:S.248, D:S.248, D:S.324, D:S.324, D:S.328, D:S.328 Salt bridges: D:R.330, D:R.330, E:K.43 pi-Cation interactions: D:R.330 ADP.20: 15 residues within 4Å: Chain E: N.127, G.129, F.198, Y.200, N.246, L.247, S.248, F.250, S.324, I.327, S.328, R.330 Chain F: K.43, K.48, M.50 13 PLIP interactions: 3 interactions with chain F, 10 interactions with chain E Salt bridges: F:K.43, F:K.43, F:K.48, E:R.330 Hydrogen bonds: E:N.127, E:G.129, E:F.198, E:Y.200, E:S.248, E:S.324, E:I.327, E:S.328, E:R.330 ADP.25: 13 residues within 4Å: Chain A: K.43, M.50 Chain F: G.129, E.131, E.183, F.198, Y.200, N.246, S.248, S.324, I.327, S.328, R.330 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:G.129, F:E.131, F:F.198, F:N.246, F:S.248, F:S.324, F:I.327, F:R.330 Salt bridges: F:R.330, F:R.330, A:K.43, A:K.43 ADP.29: 14 residues within 4Å: Chain G: N.127, G.129, F.198, K.199, Y.200, N.246, S.248, F.250, S.324, I.327, S.328, R.330 Chain H: K.43, M.50 13 PLIP interactions: 11 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:F.198, G:Y.200, G:S.248, G:S.248, G:N.255, G:S.324, G:S.328, G:R.330, G:R.330 Salt bridges: G:R.330, H:K.43, H:K.43 pi-Cation interactions: G:R.330 ADP.35: 16 residues within 4Å: Chain H: N.127, G.129, E.183, F.198, K.199, Y.200, N.246, S.248, N.255, S.324, I.327, S.328, T.329, R.330 Chain I: K.43, M.50 13 PLIP interactions: 3 interactions with chain I, 10 interactions with chain H Hydrogen bonds: I:K.48, H:G.129, H:F.198, H:S.248, H:S.248, H:N.255, H:S.324, H:S.328 Salt bridges: I:K.43, I:K.43, H:R.330, H:R.330 pi-Stacking: H:Y.200 ADP.39: 14 residues within 4Å: Chain I: N.127, G.129, F.198, Y.200, N.246, L.247, S.248, N.255, S.324, I.327, S.328, R.330 Chain J: K.43, M.50 14 PLIP interactions: 12 interactions with chain I, 2 interactions with chain J Hydrogen bonds: I:G.129, I:F.198, I:N.246, I:S.248, I:N.255, I:S.324, I:S.324, I:I.327, I:S.328, J:Y.68 Salt bridges: I:R.330, I:R.330, J:K.43 pi-Stacking: I:Y.200 ADP.43: 14 residues within 4Å: Chain J: G.129, E.183, D.197, F.198, K.199, Y.200, N.246, S.248, S.324, I.327, S.328, R.330 Chain K: K.43, M.50 11 PLIP interactions: 10 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:F.198, J:S.248, J:S.248, J:S.324, J:S.324, J:S.328, J:S.328 Salt bridges: J:R.330, J:R.330, K:K.43 pi-Cation interactions: J:R.330 ADP.47: 15 residues within 4Å: Chain K: N.127, G.129, F.198, Y.200, N.246, L.247, S.248, F.250, S.324, I.327, S.328, R.330 Chain L: K.43, K.48, M.50 13 PLIP interactions: 10 interactions with chain K, 3 interactions with chain L Hydrogen bonds: K:N.127, K:G.129, K:F.198, K:Y.200, K:S.248, K:S.324, K:I.327, K:S.328, K:R.330 Salt bridges: K:R.330, L:K.43, L:K.43, L:K.48 ADP.52: 13 residues within 4Å: Chain G: K.43, M.50 Chain L: G.129, E.131, E.183, F.198, Y.200, N.246, S.248, S.324, I.327, S.328, R.330 14 PLIP interactions: 12 interactions with chain L, 2 interactions with chain G Hydrogen bonds: L:G.129, L:E.131, L:E.131, L:E.183, L:F.198, L:N.246, L:S.248, L:S.324, L:I.327, L:R.330 Salt bridges: L:R.330, L:R.330, G:K.43, G:K.43

24 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: E.131, H.244, E.332 Chain B: E.64 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 A: E.133, E.188, E.195 Ligands: GLU.1 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A Metal complexes: GLU.1, A:E.188, A:E.195 MG.9: 5 residues within 4Å: Chain B: E.133, E.188, E.195, H.244 Ligands: GLU.7 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain B Metal complexes: GLU.7, B:E.133, B:E.188 MG.10: 4 residues within 4Å: Chain B: E.131, H.244, E.332 Chain C: E.64 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.131, B:E.332 MG.13: 5 residues within 4Å: Chain C: E.133, E.188, E.195 Ligands: GLU.11, MG.14 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:E.133, C:E.195, C:E.195, GLU.11 MG.14: 5 residues within 4Å: Chain C: E.131, H.244, E.332 Chain D: E.64 Ligands: MG.13 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.131, C:H.244, C:E.332 MG.17: 5 residues within 4Å: Chain D: E.133, H.186, E.188, E.195 Ligands: GLU.15 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.133, D:E.188, D:E.195, D:E.195, H2O.2 MG.18: 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:E.131, D:E.332, H2O.2 MG.21: 4 residues within 4Å: Chain E: E.131, H.244, E.332 Chain F: E.64 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Metal complexes: E:E.131, E:H.244, E:E.332, F:E.64 MG.22: 5 residues within 4Å: Chain E: E.131, E.133, E.188, E.195 Ligands: GLU.19 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:E.133, E:E.188, E:E.195, GLU.19 MG.26: 4 residues within 4Å: Chain A: E.64 Chain F: E.131, H.244, E.332 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.131, F:E.131, F:H.244, F:E.332, F:E.332 MG.27: 5 residues within 4Å: Chain F: E.131, E.133, E.188, E.195 Ligands: GLU.24 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.188, F:E.195 MG.30: 4 residues within 4Å: Chain G: E.131, H.244, E.332 Chain H: E.64 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.131, G:H.244, G:E.332 MG.31: 4 residues within 4Å: Chain G: E.133, E.188, E.195 Ligands: GLU.28 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:E.188, G:E.195 MG.36: 5 residues within 4Å: Chain H: E.133, E.188, E.195, H.244 Ligands: GLU.34 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Ligand interactions Metal complexes: H:E.133, H:E.188, GLU.34 MG.37: 4 residues within 4Å: Chain H: E.131, H.244, E.332 Chain I: E.64 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:E.131, H:E.332 MG.40: 5 residues within 4Å: Chain I: E.133, E.188, E.195 Ligands: GLU.38, MG.41 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain I Metal complexes: GLU.38, I:E.133, I:E.195, I:E.195 MG.41: 5 residues within 4Å: Chain I: E.131, H.244, E.332 Chain J: E.64 Ligands: MG.40 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.131, I:H.244, I:E.332 MG.44: 5 residues within 4Å: Chain J: E.133, H.186, E.188, E.195 Ligands: GLU.42 5 PLIP interactions: 3 interactions with chain J, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: J:E.188, J:E.195, J:E.195, GLU.42, H2O.4 MG.45: 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:E.131, J:E.332, H2O.4 MG.48: 4 residues within 4Å: Chain K: E.131, H.244, E.332 Chain L: E.64 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain L Metal complexes: K:E.131, K:H.244, K:E.332, L:E.64 MG.49: 5 residues within 4Å: Chain K: E.131, E.133, E.188, E.195 Ligands: GLU.46 4 PLIP interactions: 3 interactions with chain K, 1 Ligand-Ligand interactions Metal complexes: K:E.133, K:E.188, K:E.195, GLU.46 MG.53: 4 residues within 4Å: Chain G: E.64 Chain L: E.131, H.244, E.332 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:E.131, L:E.131, L:H.244, L:E.332, L:E.332 MG.54: 5 residues within 4Å: Chain L: E.131, E.133, E.188, E.195 Ligands: GLU.51 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:E.188, L:E.195

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 5 residues within 4Å: Chain A: N.47, K.48, Y.68, Y.70, G.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.70 Salt bridges: A:K.48 SO4.6: 6 residues within 4Å: Chain A: D.72, N.74, T.75, R.108, R.205, D.208 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.108, A:D.208 Water bridges: A:R.205 SO4.23: 7 residues within 4Å: Chain E: N.16, T.82, A.83, E.84, K.85, G.86, K.87 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.16 Salt bridges: E:K.87 SO4.32: 5 residues within 4Å: Chain G: N.47, K.48, Y.68, Y.70, G.100 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:Y.70, G:Y.70 Salt bridges: G:K.48 SO4.33: 6 residues within 4Å: Chain G: D.72, N.74, T.75, R.108, R.205, D.208 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:R.108, G:D.208, G:D.208 Water bridges: G:R.205 SO4.50: 7 residues within 4Å: Chain K: N.16, T.82, A.83, E.84, K.85, G.86, K.87 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:N.16 Salt bridges: K:K.87

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

2013-10-30

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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