SMTL ID : 2vdc.1

THE 9.5 A RESOLUTION STRUCTURE OF GLUTAMATE SYNTHASE FROM CRYO-ELECTRON MICROSCOPY AND ITS OLIGOMERIZATION BEHAVIOR IN SOLUTION: FUNCTIONAL IMPLICATIONS.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 9.50 Å

Oligo State

hetero-6-6-mer

Ligands

6 x OMT: S-DIOXYMETHIONINE(Non-covalent)

OMT.1: 12 residues within 4Å: Chain A: C.1, Q.209, R.210, Y.211, Q.223, H.230, N.231, G.232, E.233, S.272, D.273, S.274 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.223, A:G.232, A:S.272 Salt bridges: A:R.210 OMT.5: 10 residues within 4Å: Chain B: C.1, Q.209, R.210, Y.211, Q.223, N.231, G.232, E.233, D.273, S.274 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.223, B:G.232, B:S.274 Salt bridges: B:R.210 OMT.9: 12 residues within 4Å: Chain C: C.1, Q.209, R.210, Y.211, Q.223, H.230, N.231, G.232, E.233, S.272, D.273, S.274 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.223, C:G.232, C:S.272 Salt bridges: C:R.210 OMT.13: 10 residues within 4Å: Chain D: C.1, Q.209, R.210, Y.211, Q.223, N.231, G.232, E.233, D.273, S.274 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.223, D:G.232, D:S.274 Salt bridges: D:R.210 OMT.17: 12 residues within 4Å: Chain E: C.1, Q.209, R.210, Y.211, Q.223, H.230, N.231, G.232, E.233, S.272, D.273, S.274 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.223, E:G.232, E:S.272 Salt bridges: E:R.210 OMT.21: 10 residues within 4Å: Chain F: C.1, Q.209, R.210, Y.211, Q.223, N.231, G.232, E.233, D.273, S.274 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.223, F:G.232, F:S.274 Salt bridges: F:R.210

6 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 20 residues within 4Å: Chain A: M.479, P.856, G.857, M.858, S.859, G.885, E.886, Q.909, K.931, K.999, G.1028, G.1029, T.1030, G.1031, D.1070, G.1071, G.1072, G.1093, T.1094 Ligands: AKG.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:M.858 Hydrogen bonds: A:G.857, A:G.857, A:S.859, A:E.886, A:E.886, A:Q.909, A:Q.909, A:K.999, A:K.999, A:K.999, A:S.1027, A:G.1029, A:G.1029, A:G.1071, A:G.1072, A:G.1093, A:T.1094, A:T.1094 FMN.6: 21 residues within 4Å: Chain B: P.856, G.857, M.858, S.859, G.885, E.886, Q.909, K.931, K.999, S.1024, S.1027, G.1028, G.1029, T.1030, G.1031, D.1070, G.1071, G.1072, G.1093, T.1094 Ligands: AKG.7 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:M.858 Hydrogen bonds: B:G.857, B:S.859, B:E.886, B:Q.909, B:Q.909, B:K.999, B:K.999, B:K.999, B:K.999, B:S.1024, B:G.1029, B:G.1071, B:G.1072, B:G.1093, B:T.1094, B:T.1094, B:T.1094 FMN.10: 20 residues within 4Å: Chain C: M.479, P.856, G.857, M.858, S.859, G.885, E.886, Q.909, K.931, K.999, G.1028, G.1029, T.1030, G.1031, D.1070, G.1071, G.1072, G.1093, T.1094 Ligands: AKG.11 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:M.858 Hydrogen bonds: C:G.857, C:G.857, C:S.859, C:E.886, C:E.886, C:Q.909, C:Q.909, C:K.999, C:K.999, C:K.999, C:S.1027, C:G.1029, C:G.1029, C:G.1071, C:G.1072, C:G.1093, C:T.1094, C:T.1094 FMN.14: 21 residues within 4Å: Chain D: P.856, G.857, M.858, S.859, G.885, E.886, Q.909, K.931, K.999, S.1024, S.1027, G.1028, G.1029, T.1030, G.1031, D.1070, G.1071, G.1072, G.1093, T.1094 Ligands: AKG.15 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:M.858 Hydrogen bonds: D:G.857, D:S.859, D:E.886, D:Q.909, D:Q.909, D:K.999, D:K.999, D:K.999, D:K.999, D:S.1024, D:G.1029, D:G.1071, D:G.1072, D:G.1093, D:T.1094, D:T.1094, D:T.1094 FMN.18: 20 residues within 4Å: Chain E: M.479, P.856, G.857, M.858, S.859, G.885, E.886, Q.909, K.931, K.999, G.1028, G.1029, T.1030, G.1031, D.1070, G.1071, G.1072, G.1093, T.1094 Ligands: AKG.19 19 PLIP interactions: 19 interactions with chain E Hydrophobic interactions: E:M.858 Hydrogen bonds: E:G.857, E:G.857, E:S.859, E:E.886, E:E.886, E:Q.909, E:Q.909, E:K.999, E:K.999, E:K.999, E:S.1027, E:G.1029, E:G.1029, E:G.1071, E:G.1072, E:G.1093, E:T.1094, E:T.1094 FMN.22: 21 residues within 4Å: Chain F: P.856, G.857, M.858, S.859, G.885, E.886, Q.909, K.931, K.999, S.1024, S.1027, G.1028, G.1029, T.1030, G.1031, D.1070, G.1071, G.1072, G.1093, T.1094 Ligands: AKG.23 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:M.858 Hydrogen bonds: F:G.857, F:S.859, F:E.886, F:Q.909, F:Q.909, F:K.999, F:K.999, F:K.999, F:K.999, F:S.1024, F:G.1029, F:G.1071, F:G.1072, F:G.1093, F:T.1094, F:T.1094, F:T.1094

6 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.3: 13 residues within 4Å: Chain A: S.859, A.862, E.886, Q.934, K.937, G.942, Q.943, L.944, R.957, T.1030, G.1031, A.1032 Ligands: FMN.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.859, A:S.859, A:A.862, A:Q.934, A:K.937, A:K.937, A:Q.943, A:T.1030, A:G.1031, A:A.1032 Salt bridges: A:K.937, A:R.957 AKG.7: 13 residues within 4Å: Chain B: S.859, A.862, E.886, Q.934, K.937, G.942, Q.943, L.944, R.957, T.1030, G.1031, A.1032 Ligands: FMN.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:E.886 Hydrogen bonds: B:S.859, B:S.859, B:A.862, B:Q.934, B:K.937, B:K.937, B:Q.943, B:G.1031, B:A.1032 Salt bridges: B:K.937, B:R.957 AKG.11: 13 residues within 4Å: Chain C: S.859, A.862, E.886, Q.934, K.937, G.942, Q.943, L.944, R.957, T.1030, G.1031, A.1032 Ligands: FMN.10 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.859, C:S.859, C:A.862, C:Q.934, C:K.937, C:K.937, C:Q.943, C:T.1030, C:G.1031, C:A.1032 Salt bridges: C:K.937, C:R.957 AKG.15: 13 residues within 4Å: Chain D: S.859, A.862, E.886, Q.934, K.937, G.942, Q.943, L.944, R.957, T.1030, G.1031, A.1032 Ligands: FMN.14 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:E.886 Hydrogen bonds: D:S.859, D:S.859, D:A.862, D:Q.934, D:K.937, D:K.937, D:Q.943, D:G.1031, D:A.1032 Salt bridges: D:K.937, D:R.957 AKG.19: 13 residues within 4Å: Chain E: S.859, A.862, E.886, Q.934, K.937, G.942, Q.943, L.944, R.957, T.1030, G.1031, A.1032 Ligands: FMN.18 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:S.859, E:S.859, E:A.862, E:Q.934, E:K.937, E:K.937, E:Q.943, E:T.1030, E:G.1031, E:A.1032 Salt bridges: E:K.937, E:R.957 AKG.23: 13 residues within 4Å: Chain F: S.859, A.862, E.886, Q.934, K.937, G.942, Q.943, L.944, R.957, T.1030, G.1031, A.1032 Ligands: FMN.22 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:E.886 Hydrogen bonds: F:S.859, F:S.859, F:A.862, F:Q.934, F:K.937, F:K.937, F:Q.943, F:G.1031, F:A.1032 Salt bridges: F:K.937, F:R.957

6 x F3S: FE3-S4 CLUSTER(Covalent)(Non-covalent)

F3S.4: 11 residues within 4Å: Chain A: C.1102, I.1103, M.1104, V.1105, R.1106, Q.1107, C.1108, C.1113, V.1117, C.1118 Chain J: Q.87 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.1102, A:C.1108, A:C.1113, F3S.4 F3S.8: 10 residues within 4Å: Chain B: C.1102, I.1103, M.1104, V.1105, R.1106, Q.1107, C.1108, C.1113, V.1117, C.1118 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.1102, B:C.1108, B:C.1113 F3S.12: 11 residues within 4Å: Chain C: C.1102, I.1103, M.1104, V.1105, R.1106, Q.1107, C.1108, C.1113, V.1117, C.1118 Chain K: Q.87 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:C.1102, C:C.1108, C:C.1113, F3S.12 F3S.16: 10 residues within 4Å: Chain D: C.1102, I.1103, M.1104, V.1105, R.1106, Q.1107, C.1108, C.1113, V.1117, C.1118 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.1102, D:C.1108, D:C.1113 F3S.20: 11 residues within 4Å: Chain E: C.1102, I.1103, M.1104, V.1105, R.1106, Q.1107, C.1108, C.1113, V.1117, C.1118 Chain L: Q.87 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:C.1102, E:C.1108, E:C.1113, F3S.20 F3S.24: 10 residues within 4Å: Chain F: C.1102, I.1103, M.1104, V.1105, R.1106, Q.1107, C.1108, C.1113, V.1117, C.1118 3 PLIP interactions: 3 interactions with chain F, Metal complexes: F:C.1102, F:C.1108, F:C.1113

12 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.25: 12 residues within 4Å: Chain G: C.34, P.35, V.36, I.40, W.43, N.63, C.69, C.73, Q.75, L.78, C.79, E.99 9 PLIP interactions: 7 interactions with chain G, 2 Ligand-Ligand interactions Salt bridges: G:E.99, G:E.99, G:E.99 Metal complexes: G:C.34, G:C.73, G:C.79, G:E.99, SF4.25, SF4.25 SF4.26: 10 residues within 4Å: Chain G: C.22, S.23, Q.24, C.25, C.30, C.83, V.84, I.85, V.93, I.95 6 PLIP interactions: 4 interactions with chain G, 2 Ligand-Ligand interactions Metal complexes: G:C.22, G:C.25, G:C.30, G:C.83, SF4.26, SF4.26 SF4.28: 12 residues within 4Å: Chain H: C.34, P.35, V.36, I.40, W.43, N.63, C.69, C.73, Q.75, L.78, C.79, E.99 9 PLIP interactions: 7 interactions with chain H, 2 Ligand-Ligand interactions Salt bridges: H:E.99, H:E.99, H:E.99 Metal complexes: H:C.34, H:C.73, H:C.79, H:E.99, SF4.28, SF4.28 SF4.29: 10 residues within 4Å: Chain H: C.22, S.23, Q.24, C.25, C.30, C.83, V.84, I.85, V.93, I.95 6 PLIP interactions: 4 interactions with chain H, 2 Ligand-Ligand interactions Metal complexes: H:C.22, H:C.25, H:C.30, H:C.83, SF4.29, SF4.29 SF4.31: 12 residues within 4Å: Chain I: C.34, P.35, V.36, I.40, W.43, N.63, C.69, C.73, Q.75, L.78, C.79, E.99 9 PLIP interactions: 7 interactions with chain I, 2 Ligand-Ligand interactions Salt bridges: I:E.99, I:E.99, I:E.99 Metal complexes: I:C.34, I:C.73, I:C.79, I:E.99, SF4.31, SF4.31 SF4.32: 10 residues within 4Å: Chain I: C.22, S.23, Q.24, C.25, C.30, C.83, V.84, I.85, V.93, I.95 6 PLIP interactions: 4 interactions with chain I, 2 Ligand-Ligand interactions Metal complexes: I:C.22, I:C.25, I:C.30, I:C.83, SF4.32, SF4.32 SF4.34: 12 residues within 4Å: Chain J: C.34, P.35, V.36, I.40, W.43, N.63, C.69, C.73, Q.75, L.78, C.79, E.99 9 PLIP interactions: 7 interactions with chain J, 2 Ligand-Ligand interactions Salt bridges: J:E.99, J:E.99, J:E.99 Metal complexes: J:C.34, J:C.73, J:C.79, J:E.99, SF4.34, SF4.34 SF4.35: 10 residues within 4Å: Chain J: C.22, S.23, Q.24, C.25, C.30, C.83, V.84, I.85, V.93, I.95 6 PLIP interactions: 4 interactions with chain J, 2 Ligand-Ligand interactions Metal complexes: J:C.22, J:C.25, J:C.30, J:C.83, SF4.35, SF4.35 SF4.37: 12 residues within 4Å: Chain K: C.34, P.35, V.36, I.40, W.43, N.63, C.69, C.73, Q.75, L.78, C.79, E.99 9 PLIP interactions: 7 interactions with chain K, 2 Ligand-Ligand interactions Salt bridges: K:E.99, K:E.99, K:E.99 Metal complexes: K:C.34, K:C.73, K:C.79, K:E.99, SF4.37, SF4.37 SF4.38: 10 residues within 4Å: Chain K: C.22, S.23, Q.24, C.25, C.30, C.83, V.84, I.85, V.93, I.95 6 PLIP interactions: 4 interactions with chain K, 2 Ligand-Ligand interactions Metal complexes: K:C.22, K:C.25, K:C.30, K:C.83, SF4.38, SF4.38 SF4.40: 12 residues within 4Å: Chain L: C.34, P.35, V.36, I.40, W.43, N.63, C.69, C.73, Q.75, L.78, C.79, E.99 9 PLIP interactions: 7 interactions with chain L, 2 Ligand-Ligand interactions Salt bridges: L:E.99, L:E.99, L:E.99 Metal complexes: L:C.34, L:C.73, L:C.79, L:E.99, SF4.40, SF4.40 SF4.41: 10 residues within 4Å: Chain L: C.22, S.23, Q.24, C.25, C.30, C.83, V.84, I.85, V.93, I.95 6 PLIP interactions: 4 interactions with chain L, 2 Ligand-Ligand interactions Metal complexes: L:C.22, L:C.25, L:C.30, L:C.83, SF4.41, SF4.41

6 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.27: 34 residues within 4Å: Chain G: I.72, P.74, I.128, G.129, A.130, G.131, P.132, A.133, Y.151, D.152, R.153, Y.154, G.159, L.160, I.165, K.169, F.193, E.194, V.195, A.214, T.215, G.216, L.240, D.274, T.275, D.278, F.376, N.383, G.416, D.417, S.423, L.424, V.425, A.428 17 PLIP interactions: 17 interactions with chain G Hydrophobic interactions: G:I.165, G:L.240, G:F.376 Hydrogen bonds: G:I.72, G:A.130, G:A.133, G:R.153, G:R.153, G:G.159, G:L.160, G:K.169, G:V.195, G:V.195, G:D.274, G:D.417, G:S.423, G:V.425 FAD.30: 34 residues within 4Å: Chain H: I.72, P.74, I.128, G.129, A.130, G.131, P.132, A.133, Y.151, D.152, R.153, Y.154, G.159, L.160, I.165, K.169, F.193, E.194, V.195, A.214, T.215, G.216, L.240, D.274, T.275, D.278, F.376, N.383, G.416, D.417, S.423, L.424, V.425, A.428 17 PLIP interactions: 17 interactions with chain H Hydrophobic interactions: H:I.165, H:L.240, H:F.376 Hydrogen bonds: H:I.72, H:A.130, H:A.133, H:R.153, H:R.153, H:G.159, H:L.160, H:K.169, H:V.195, H:V.195, H:D.274, H:D.417, H:S.423, H:V.425 FAD.33: 34 residues within 4Å: Chain I: I.72, P.74, I.128, G.129, A.130, G.131, P.132, A.133, Y.151, D.152, R.153, Y.154, G.159, L.160, I.165, K.169, F.193, E.194, V.195, A.214, T.215, G.216, L.240, D.274, T.275, D.278, F.376, N.383, G.416, D.417, S.423, L.424, V.425, A.428 17 PLIP interactions: 17 interactions with chain I Hydrophobic interactions: I:I.165, I:L.240, I:F.376 Hydrogen bonds: I:I.72, I:A.130, I:A.133, I:R.153, I:R.153, I:G.159, I:L.160, I:K.169, I:V.195, I:V.195, I:D.274, I:D.417, I:S.423, I:V.425 FAD.36: 34 residues within 4Å: Chain J: I.72, P.74, I.128, G.129, A.130, G.131, P.132, A.133, Y.151, D.152, R.153, Y.154, G.159, L.160, I.165, K.169, F.193, E.194, V.195, A.214, T.215, G.216, L.240, D.274, T.275, D.278, F.376, N.383, G.416, D.417, S.423, L.424, V.425, A.428 17 PLIP interactions: 17 interactions with chain J Hydrophobic interactions: J:I.165, J:L.240, J:F.376 Hydrogen bonds: J:I.72, J:A.130, J:A.133, J:R.153, J:R.153, J:G.159, J:L.160, J:K.169, J:V.195, J:V.195, J:T.215, J:D.417, J:S.423, J:V.425 FAD.39: 34 residues within 4Å: Chain K: I.72, P.74, I.128, G.129, A.130, G.131, P.132, A.133, Y.151, D.152, R.153, Y.154, G.159, L.160, I.165, K.169, F.193, E.194, V.195, A.214, T.215, G.216, L.240, D.274, T.275, D.278, F.376, N.383, G.416, D.417, S.423, L.424, V.425, A.428 17 PLIP interactions: 17 interactions with chain K Hydrophobic interactions: K:I.165, K:L.240, K:F.376 Hydrogen bonds: K:I.72, K:A.130, K:A.133, K:R.153, K:R.153, K:G.159, K:L.160, K:K.169, K:V.195, K:V.195, K:T.215, K:D.417, K:S.423, K:V.425 FAD.42: 34 residues within 4Å: Chain L: I.72, P.74, I.128, G.129, A.130, G.131, P.132, A.133, Y.151, D.152, R.153, Y.154, G.159, L.160, I.165, K.169, F.193, E.194, V.195, A.214, T.215, G.216, L.240, D.274, T.275, D.278, F.376, N.383, G.416, D.417, S.423, L.424, V.425, A.428 17 PLIP interactions: 17 interactions with chain L Hydrophobic interactions: L:I.165, L:L.240, L:F.376 Hydrogen bonds: L:I.72, L:A.130, L:A.133, L:R.153, L:R.153, L:G.159, L:L.160, L:K.169, L:V.195, L:V.195, L:T.215, L:D.417, L:S.423, L:V.425

Links

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Citation

Cottevieille, M. et al., The Subnanometer Resolution Structure of the Glutamate Synthase 1.2-Mda Hexamer by Cryoelectron Microscopy and its Oligomerization Behavior in Solution: Functional Implications. J.Biol.Chem. (2008)

Release Date

2008-01-15

Peptides

GLUTAMATE SYNTHASE [NADPH] LARGE CHAIN: ABCDEF
GLUTAMATE SYNTHASE [NADPH] SMALL CHAIN: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

GLUTAMATE SYNTHASE [NADPH] LARGE CHAIN

GLUTAMATE SYNTHASE [NADPH] SMALL CHAIN