SMTL ID : 7mfm.1

Glutamate synthase, glutamate dehydrogenase counter-enzyme complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-2-2-mer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 25 residues within 4Å: Chain B: M.493, G.867, A.868, M.869, S.870, S.873, L.874, E.897, Q.920, K.942, Q.945, K.1010, S.1035, D.1038, G.1039, G.1040, T.1041, G.1042, D.1081, G.1082, K.1083, F.1103, A.1104, T.1105, L.1108 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:A.868, B:S.870, B:E.897, B:Q.920, B:K.942, B:K.1010, B:D.1038, B:G.1040, B:G.1040, B:G.1082, B:K.1083, B:A.1104, B:T.1105, B:T.1105 Salt bridges: B:K.1083 FMN.3: 25 residues within 4Å: Chain C: M.493, G.867, A.868, M.869, S.870, S.873, L.874, E.897, Q.920, K.942, Q.945, K.1010, S.1035, D.1038, G.1039, G.1040, T.1041, G.1042, D.1081, G.1082, K.1083, F.1103, A.1104, T.1105, L.1108 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:A.868, C:S.870, C:E.897, C:Q.920, C:K.942, C:K.1010, C:D.1038, C:G.1040, C:G.1040, C:G.1082, C:K.1083, C:A.1104, C:T.1105, C:T.1105 Salt bridges: C:K.1083

2 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.2: 13 residues within 4Å: Chain B: M.493, C.1113, V.1114, M.1115, M.1116, R.1117, A.1118, C.1119, C.1124, P.1125, V.1126, V.1128, A.1129 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.1113, B:C.1119, B:C.1124 F3S.4: 13 residues within 4Å: Chain C: M.493, C.1113, V.1114, M.1115, M.1116, R.1117, A.1118, C.1119, C.1124, P.1125, V.1126, V.1128, A.1129 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.1113, C:C.1119, C:C.1124

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

FAD.5: 38 residues within 4Å: Chain D: V.105, C.106, P.107, V.158, G.159, S.160, G.161, P.162, A.163, G.164, F.181, E.182, R.183, G.189, L.190, G.194, I.195, K.199, T.223, E.224, I.225, C.244, T.245, G.246, A.247, Q.248, M.267, D.302, T.303, D.306, F.421, L.429, D.460, Q.465, S.466, L.467, I.468, A.471 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:V.105, D:I.195, D:D.302, D:I.468 Hydrogen bonds: D:G.159, D:S.160, D:G.161, D:A.163, D:E.182, D:E.182, D:R.183, D:R.183, D:L.190, D:E.224, D:A.247, D:Q.248, D:D.460, D:D.460, D:D.460, D:Q.465, D:S.466, D:S.466 pi-Cation interactions: D:R.183 FAD.8: 38 residues within 4Å: Chain E: V.105, C.106, P.107, V.158, G.159, S.160, G.161, P.162, A.163, G.164, F.181, E.182, R.183, G.189, L.190, G.194, I.195, K.199, T.223, E.224, I.225, C.244, T.245, G.246, A.247, Q.248, M.267, D.302, T.303, D.306, F.421, L.429, D.460, Q.465, S.466, L.467, I.468, A.471 23 PLIP interactions: 23 interactions with chain E Hydrophobic interactions: E:V.105, E:I.195, E:D.302, E:I.468 Hydrogen bonds: E:G.159, E:S.160, E:G.161, E:A.163, E:E.182, E:E.182, E:R.183, E:R.183, E:L.190, E:E.224, E:A.247, E:Q.248, E:D.460, E:D.460, E:D.460, E:Q.465, E:S.466, E:S.466 pi-Cation interactions: E:R.183

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

SF4.6: 14 residues within 4Å: Chain D: C.46, M.47, D.48, C.49, P.52, F.53, C.54, I.73, P.74, C.114, T.115, L.116, V.123, I.125 7 PLIP interactions: 7 interactions with chain D, Metal complexes: D:C.46, D:C.49, D:C.49, D:C.54, D:C.54, D:C.114, D:T.115 SF4.7: 13 residues within 4Å: Chain D: C.67, N.71, I.73, W.76, T.102, C.106, A.108, P.109, C.110, I.125, K.126, E.129, V.469 7 PLIP interactions: 7 interactions with chain D, Salt bridges: D:E.129, D:E.129, D:E.129 Metal complexes: D:C.67, D:C.106, D:C.110, D:E.129 SF4.9: 14 residues within 4Å: Chain E: C.46, M.47, D.48, C.49, P.52, F.53, C.54, I.73, P.74, C.114, T.115, L.116, V.123, I.125 7 PLIP interactions: 7 interactions with chain E, Metal complexes: E:C.46, E:C.49, E:C.49, E:C.54, E:C.54, E:C.114, E:T.115 SF4.10: 13 residues within 4Å: Chain E: C.67, N.71, I.73, W.76, T.102, C.106, A.108, P.109, C.110, I.125, K.126, E.129, V.469 7 PLIP interactions: 7 interactions with chain E, Salt bridges: E:E.129, E:E.129, E:E.129 Metal complexes: E:C.67, E:C.106, E:C.110, E:E.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jayaraman, V. et al., A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis. Nat.Chem.Biol. (2022)

Release Date

2022-01-05

Peptides

Glutamate dehydrogenase: AFGHIJ
Glutamate synthase (NADPH) large chain: BC
Glutamate synthase (NADPH) small chain: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
B

G
C

H
D

I
E

J
F

B
G

C
H

D
I

E
J

Glutamate dehydrogenase

Glutamate synthase (NADPH) large chain

Glutamate synthase (NADPH) small chain

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