SMTL ID : 9hiq.1

MnmE-MnmG a4b2 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-mer

Ligands

4 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 24 residues within 4Å: Chain A: R.224, P.225, N.226, A.227, G.228, K.229, S.230, S.231, V.244, T.245, D.246, T.250, T.251, D.270, T.271, A.272, G.273, N.335, K.336, D.338, I.339, S.358, A.359, R.360 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:R.224, A:N.226, A:N.226, A:A.227, A:G.228, A:K.229, A:K.229, A:S.230, A:S.230, A:S.230, A:S.230, A:S.231, A:S.231, A:T.245, A:T.245, A:T.250, A:T.250, A:T.251, A:T.271, A:T.271, A:T.271, A:N.335, A:K.336, A:K.336, A:A.359, A:R.360, A:R.360, A:R.360 Salt bridges: A:D.338 GNP.2: 25 residues within 4Å: Chain B: P.225, N.226, A.227, G.228, K.229, S.230, S.231, I.243, V.244, T.245, D.246, I.247, G.249, T.250, T.251, T.271, A.272, G.273, N.335, K.336, D.338, I.339, S.358, A.359, R.360 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:N.226, B:N.226, B:G.228, B:K.229, B:S.230, B:S.230, B:S.230, B:S.230, B:S.231, B:T.245, B:G.249, B:T.250, B:T.250, B:T.251, B:T.251, B:G.273, B:N.335, B:K.336, B:A.359, B:R.360 Salt bridges: B:K.229, B:D.338 GNP.5: 24 residues within 4Å: Chain E: P.225, N.226, A.227, G.228, K.229, S.230, S.231, I.243, V.244, T.245, D.246, I.247, A.248, G.249, T.250, T.251, G.273, N.335, K.336, D.338, I.339, S.358, A.359, R.360 24 PLIP interactions: 24 interactions with chain E Hydrogen bonds: E:N.226, E:N.226, E:A.227, E:G.228, E:K.229, E:K.229, E:K.229, E:S.230, E:S.230, E:I.243, E:T.245, E:T.245, E:G.249, E:T.250, E:T.250, E:T.251, E:T.251, E:G.273, E:N.335, E:K.336, E:A.359, E:R.360, E:R.360 Salt bridges: E:D.338 GNP.6: 22 residues within 4Å: Chain F: R.224, P.225, N.226, A.227, G.228, K.229, S.230, S.231, I.243, V.244, T.245, D.246, T.250, T.251, N.335, K.336, D.338, L.357, S.358, A.359, R.360, T.361 23 PLIP interactions: 23 interactions with chain F Hydrogen bonds: F:R.224, F:N.226, F:A.227, F:G.228, F:K.229, F:S.230, F:S.230, F:S.231, F:S.231, F:T.245, F:T.250, F:T.251, F:T.251, F:N.335, F:K.336, F:A.359, F:R.360, F:R.360, F:R.360, F:T.361, F:T.361 Salt bridges: F:D.338 pi-Cation interactions: F:K.336

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

FAD.3: 29 residues within 4Å: Chain B: K.454 Chain C: I.32, G.33, G.34, G.35, H.36, L.55, T.56, H.57, S.66, C.67, V.145, T.174, V.175, G.176, T.177, F.178, R.194, L.203, T.219, G.220, T.221, Y.361, I.363, Q.390, T.395, G.396, Y.397, A.400 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:R.194, C:T.219, C:T.221, C:Y.361, C:I.363 Hydrogen bonds: C:G.34, C:H.36, C:A.37, C:H.57, C:H.57, C:T.177, C:T.177, C:S.200, C:S.200, C:Q.390, C:T.395, C:G.396, B:K.454 Salt bridges: C:H.36, C:R.194 pi-Cation interactions: C:H.57, C:H.57 FAD.4: 31 residues within 4Å: Chain D: I.32, G.33, G.34, G.35, H.36, A.37, L.55, T.56, H.57, S.66, C.67, V.145, T.174, V.175, G.176, T.177, F.178, R.194, L.203, T.219, G.220, T.221, Y.361, I.363, G.389, Q.390, T.395, G.396, Y.397, A.400 Chain E: K.454 19 PLIP interactions: 18 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:T.219, D:T.221, D:Y.361, D:I.363 Hydrogen bonds: D:H.36, D:A.37, D:T.56, D:H.57, D:H.57, D:T.177, D:Q.390, D:T.395, D:T.395, D:G.396, E:K.454 Salt bridges: D:H.36, D:R.194 pi-Cation interactions: D:H.57, D:H.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maes, L. et al., Cryo-EM structures of the MnmE-MnmG complex reveal large conformational changes and provide new insights into the mechanism of tRNA modification. Nucleic Acids Res. (2025)

Release Date

2025-08-27

Peptides

tRNA modification GTPase MnmE: ABEF
tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
E

F
F

C
C

D
D

tRNA modification GTPase MnmE

tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG

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