SMTL ID : 2x7j.1

STRUCTURE OF THE MENAQUINONE BIOSYNTHESIS PROTEIN MEND FROM BACILLUS SUBTILIS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 24 residues within 4Å: Chain A: S.429, M.430, N.455, G.456, I.457, D.458, G.480, D.481, L.482, S.483, H.486, N.508, G.510, G.511, G.512, I.513, F.514 Chain B: P.53, E.78, T.101, A.105, Q.141 Ligands: MN.2, EDO.9 24 PLIP interactions: 20 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.457, A:D.458, A:F.514, A:F.514, B:P.53 Hydrogen bonds: A:S.429, A:S.429, A:M.430, A:N.455, A:I.457, A:D.481, A:L.482, A:S.483, A:N.508, A:G.512, A:I.513 Water bridges: A:G.480, A:S.483, A:N.508, A:N.508, B:E.78, B:A.105, B:A.105 pi-Stacking: A:F.514 TPP.7: 27 residues within 4Å: Chain A: P.53, E.78, T.101, T.104, A.105, Q.141 Chain B: E.407, S.429, M.430, P.431, N.455, G.456, I.457, D.458, G.480, D.481, L.482, S.483, H.486, N.508, G.510, G.511, G.512, I.513, F.514 Ligands: EDO.3, MN.8 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.457, B:I.457, B:D.458, B:F.514 Hydrogen bonds: B:S.429, B:M.430, B:N.455, B:I.457, B:D.481, B:L.482, B:S.483, B:G.512, B:I.513 Water bridges: B:S.429, B:G.480, B:S.483, B:N.508, B:N.508, A:A.105, A:A.105 TPP.13: 26 residues within 4Å: Chain C: S.429, M.430, P.431, N.455, G.456, I.457, D.458, G.480, D.481, L.482, S.483, H.486, N.508, G.510, G.511, G.512, I.513, F.514 Chain D: P.53, E.78, T.101, T.104, A.105, Q.141 Ligands: MN.14, EDO.21 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.457, C:D.458, C:F.514, C:F.514, D:P.53 Hydrogen bonds: C:S.429, C:S.429, C:M.430, C:N.455, C:I.457, C:G.480, C:D.481, C:L.482, C:S.483, C:G.512, C:I.513 Water bridges: C:S.483, D:A.105, D:A.105 pi-Stacking: C:F.514 TPP.19: 26 residues within 4Å: Chain C: P.53, E.78, T.101, T.104, A.105, Q.141 Chain D: E.407, S.429, M.430, P.431, N.455, G.456, I.457, D.458, G.480, D.481, L.482, S.483, N.508, G.510, G.511, G.512, I.513, F.514 Ligands: EDO.15, MN.20 19 PLIP interactions: 3 interactions with chain C, 16 interactions with chain D Hydrophobic interactions: C:P.53, D:I.457, D:D.458, D:F.514 Water bridges: C:A.105, C:Q.141, D:G.480, D:S.483, D:N.508 Hydrogen bonds: D:S.429, D:M.430, D:N.455, D:I.457, D:D.481, D:L.482, D:S.483, D:N.508, D:G.512, D:I.513

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: D.481, N.508, G.510, G.512 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.481, A:G.510, H2O.237 MN.8: 5 residues within 4Å: Chain B: D.481, N.508, G.510, G.512 Ligands: TPP.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.481, B:G.510, H2O.524 MN.14: 5 residues within 4Å: Chain C: D.481, N.508, G.510, G.512 Ligands: TPP.13 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.481, C:G.510, H2O.777 MN.20: 4 residues within 4Å: Chain D: D.481, N.508, G.510 Ligands: TPP.19 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.481, D:G.510, H2O.1072

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 9 residues within 4Å: Chain A: G.54, S.55, R.56, T.101, S.102, R.130, Q.141 Chain B: F.514 Ligands: TPP.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.55, A:R.56, A:T.101, A:T.101, A:R.130, A:R.130, A:Q.141 EDO.9: 9 residues within 4Å: Chain A: F.514 Chain B: G.54, S.55, R.56, T.101, S.102, R.130, Q.141 Ligands: TPP.1 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.55, B:R.56, B:S.102, B:R.130, B:Q.141 EDO.15: 9 residues within 4Å: Chain C: G.54, S.55, R.56, T.101, S.102, R.130, Q.141 Chain D: F.514 Ligands: TPP.19 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.55, C:R.56, C:S.102, C:R.130, C:Q.141 EDO.21: 7 residues within 4Å: Chain C: F.514 Chain D: G.54, S.55, R.56, T.101, Q.141 Ligands: TPP.13 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.55, D:R.56, D:T.101, D:Q.141 Water bridges: D:S.55, D:R.56

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: C.64, A.65, H.67, I.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.70 Water bridges: A:V.72 NA.10: 4 residues within 4Å: Chain B: C.64, A.65, H.67, I.70 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.64 Water bridges: B:V.72 NA.16: 4 residues within 4Å: Chain C: C.64, A.65, H.67, I.70 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:C.64 Water bridges: C:V.72 NA.22: 4 residues within 4Å: Chain D: C.64, A.65, H.67, I.70 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.70

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

SO4.5: 7 residues within 4Å: Chain A: R.56, P.131, E.133, L.134, L.197, R.198, E.199 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.199 Water bridges: A:R.56, A:R.56 Salt bridges: A:R.56 SO4.6: 3 residues within 4Å: Chain A: K.300, F.516, R.588 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.588 Salt bridges: A:K.300, A:R.588 SO4.11: 7 residues within 4Å: Chain B: R.56, P.131, E.133, L.134, L.197, R.198, E.199 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.133, B:E.199, B:E.199 Salt bridges: B:R.56 SO4.12: 3 residues within 4Å: Chain B: K.300, F.516, R.588 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.300, B:K.300 Salt bridges: B:K.300, B:R.588 SO4.17: 7 residues within 4Å: Chain C: R.56, P.131, E.133, L.134, L.197, R.198, E.199 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.133, C:E.199, C:E.199 Water bridges: C:R.56 Salt bridges: C:R.56 SO4.18: 3 residues within 4Å: Chain C: K.300, F.516, R.588 3 PLIP interactions: 3 interactions with chain C Water bridges: C:H.587 Salt bridges: C:K.300, C:R.588 SO4.23: 7 residues within 4Å: Chain D: R.56, P.131, E.133, L.134, L.197, R.198, E.199 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:L.197, D:E.199, D:E.199 Water bridges: D:R.56, D:R.56, D:E.133 Salt bridges: D:R.56 SO4.24: 3 residues within 4Å: Chain D: K.300, F.516, R.588 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.300, D:R.588

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dawson, A. et al., Structure and Reactivity of Bacillus Subtilis Mend Catalyzing the First Committed Step in Menaquinone Biosynthesis. J.Mol.Biol. (2010)

Release Date

2010-07-14

Peptides

2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE