SMTL ID : 6e13.1

Pseudomonas putida PqqB with a non-physiological zinc at the active site binds the substrate mimic, 5-cysteinyl-3,4-dihydroxyphenylalanine (5-Cys-DOPA), non-specifically but supports the proposed function of the enzyme in pyrroloquinoline quinone biosynthesis.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.20, C.22, C.25, N.273 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.20, A:C.22, A:C.25 ZN.2: 5 residues within 4Å: Chain A: A.12, D.93, H.94, H.270 Ligands: HKS.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.94, A:H.270, H2O.2 ZN.5: 4 residues within 4Å: Chain B: C.20, C.22, C.25, N.273 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.20, B:C.22, B:C.25 ZN.6: 5 residues within 4Å: Chain B: A.12, D.93, H.94, H.270 Ligands: HKS.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.94, B:H.270, H2O.3

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 6 residues within 4Å: Chain A: Q.91, I.92, P.167, P.168 Chain B: W.132 Ligands: HKS.4 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: W.132 Chain B: Q.91, I.92, P.167, P.168 Ligands: HKS.8 Ligand excluded by PLIP

2 x HKS: 3-{[(2S)-2-amino-2-carboxyethyl]sulfanyl}-5-hydroxy-L-tyrosine(Non-covalent)

HKS.4: 16 residues within 4Å: Chain A: A.11, A.12, Q.17, Q.91, D.93, P.168, M.230, M.243, H.270, N.272, N.273 Chain B: R.78, R.102, W.132 Ligands: ZN.2, CL.3 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.12 Hydrogen bonds: A:A.12, A:G.13, A:Q.17, A:Q.17, A:Q.91, A:N.272, B:R.102, B:W.132 Water bridges: A:I.92 Salt bridges: B:R.78 HKS.8: 16 residues within 4Å: Chain A: R.78, R.102, W.132 Chain B: A.11, A.12, Q.17, Q.91, D.93, P.168, M.230, M.243, H.270, N.272, N.273 Ligands: ZN.6, CL.7 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.12 Hydrogen bonds: B:A.12, B:G.13, B:Q.17, B:Q.17, B:Q.91, B:D.93, B:N.272, B:N.273, A:R.102, A:W.132 Water bridges: B:I.92 Salt bridges: A:R.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koehn, E.M. et al., Discovery of Hydroxylase Activity for PqqB Provides a Missing Link in the Pyrroloquinoline Quinone Biosynthetic Pathway. J.Am.Chem.Soc. (2019)

Release Date

2019-05-22

Peptides

Coenzyme PQQ synthesis protein B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Coenzyme PQQ synthesis protein B