SMTL ID : 7mgn.1

Crystal structure of F501H/H506E variant of 2-ketopropyl coenzyme M oxidoreductase/carboxylase (2-KPCC) from Xanthobacter autotrophicus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x COM: 1-THIOETHANESULFONIC ACID(Non-covalent)

COM.1: 10 residues within 4Å: Chain A: A.53, R.56, F.57, G.79, C.82, P.83, M.140, M.361, R.365 Chain B: H.501 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.56, A:R.365 COM.4: 10 residues within 4Å: Chain A: H.501 Chain B: A.53, R.56, F.57, G.79, C.82, P.83, M.140, M.361, R.365 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.56 Salt bridges: B:R.56, B:R.365

2 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.2: 36 residues within 4Å: Chain A: G.50, G.51, G.52, A.53, A.54, V.72, D.73, R.74, W.75, G.80, S.81, C.82, N.85, A.86, C.87, H.90, H.91, C.156, P.157, A.158, A.181, V.182, G.183, A.184, H.202, T.225, Y.229, E.314, R.317, G.352, D.353, M.359, E.360, M.361, A.364 Chain B: H.501 31 PLIP interactions: 30 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.86, A:H.202, A:T.225, A:Y.229 Hydrogen bonds: A:G.51, A:G.52, A:A.54, A:R.74, A:R.74, A:W.75, A:W.75, A:S.81, A:S.81, A:H.90, A:A.158, A:A.184, A:R.317, A:D.353, A:M.359, A:M.361, B:H.501 Water bridges: A:A.53, A:G.80, A:C.82, A:D.353, A:D.353, A:L.354, A:L.354, A:F.362, A:A.364 pi-Cation interactions: A:K.224 FDA.5: 35 residues within 4Å: Chain A: H.501 Chain B: G.50, G.51, G.52, A.53, A.54, V.72, D.73, R.74, W.75, G.80, S.81, N.85, A.86, C.87, H.90, H.91, C.156, P.157, A.158, A.181, V.182, G.183, A.184, H.202, T.225, Y.229, E.314, R.317, G.352, D.353, M.359, E.360, M.361, A.364 33 PLIP interactions: 32 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.86, B:H.202, B:T.225 Hydrogen bonds: B:G.51, B:G.52, B:A.54, B:R.74, B:R.74, B:S.81, B:S.81, B:S.81, B:H.90, B:A.158, B:A.158, B:A.184, B:R.317, B:D.353, B:E.360, B:E.360, B:M.361, A:H.501 Water bridges: B:A.53, B:G.80, B:S.81, B:C.82, B:A.184, B:D.353, B:L.354, B:L.354, B:E.360, B:F.362 pi-Cation interactions: B:R.74, B:K.224

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: L.427, V.429, L.431, A.447, S.450 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.429, A:L.431, A:A.447, A:S.450, H2O.6 MG.6: 5 residues within 4Å: Chain B: L.427, V.429, L.431, A.447, S.450 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:V.429, B:L.431, B:A.447, B:S.450, H2O.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prussia, G.A. et al., The unique Phe-His dyad of 2-ketopropyl coenzyme M oxidoreductase/carboxylase selectively promotes carboxylation and S-C bond cleavage. J.Biol.Chem. (2021)

Release Date

2021-07-21

Peptides

2-oxopropyl-CoM reductase, carboxylating: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-oxopropyl-CoM reductase, carboxylating