SMTL ID : 4rzy.1 (1 other biounit)

Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase RlDddP in complex with MES

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

4 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: D.295, D.297, D.307, E.421 Ligands: FE.2, MES.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.295, A:D.297, A:D.307, A:E.421, H2O.1 FE.2: 6 residues within 4Å: Chain A: D.307, H.371, E.406, E.421 Ligands: FE.1, MES.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.307, A:H.371, A:E.406, A:E.421, H2O.1 FE.4: 6 residues within 4Å: Chain B: D.307, H.371, E.406, E.421 Ligands: FE.5, MES.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.307, B:H.371, B:E.406, B:E.421, H2O.26 FE.5: 6 residues within 4Å: Chain B: D.295, D.297, D.307, E.421 Ligands: FE.4, MES.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.295, B:D.297, B:D.307, B:E.421, H2O.26

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 15 residues within 4Å: Chain A: T.265, L.267, D.295, D.297, D.307, Y.366, C.368, D.377, L.381 Chain B: W.95, Y.117, F.142, D.143 Ligands: FE.1, FE.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.366, A:D.377 Salt bridges: A:D.377 MES.6: 14 residues within 4Å: Chain A: W.95, Y.117, F.142, D.143 Chain B: T.265, L.267, D.295, D.297, D.307, Y.366, C.368, D.377 Ligands: FE.4, FE.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.366, A:Y.117 Salt bridges: B:D.377

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, P. et al., Structural and molecular basis for the novel catalytic mechanism and evolution of DddP, an abundant peptidase-like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold. Mol.Microbiol. (2015)

Release Date

2015-08-05

Peptides

Peptidase M24: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Peptidase M24

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