SMTL ID : 2yor.1

Crystallization of a 45 kDa peroxygenase- peroxidase from the mushroom Agrocybe aegerita and structure determination by SAD utilizing only the haem iron

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: N.138, T.140, L.141 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 2 residues within 4Å: Chain A: F.130, N.179 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN-MAN.2: 12 residues within 4Å: Chain A: R.151, F.152, G.153, G.154, N.158, L.159, T.160, Q.210 Chain B: C.275, E.279, A.314, C.316 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4: 13 residues within 4Å: Chain B: F.130, F.131, N.138, L.141, K.168, Q.171, D.172, A.175, T.176, P.178, I.259 Ligands: SO4.30, CL.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.176 Water bridges: B:I.259

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.5: 11 residues within 4Å: Chain A: C.275, E.279, A.314, C.316, T.317 Chain B: F.152, G.153, G.154, N.158, T.160, Q.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.279 NAG-NAG.6: 2 residues within 4Å: Chain B: F.130, N.179 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: L.276, E.279, N.283, V.319, R.324 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.324 NAG-NAG.8: 2 residues within 4Å: Chain B: P.291, N.292 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.291

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.9: 27 residues within 4Å: Chain A: P.32, C.33, P.34, G.35, L.36, I.56, V.60, L.64, F.66, A.74, T.75, A.78, L.112, F.118, E.119, G.120, S.123, M.124, T.125, R.186, E.193, F.196, P.197, L.200, F.201 Ligands: MG.10, MZ0.11 31 PLIP interactions: 31 interactions with chain A, Hydrophobic interactions: A:P.34, A:L.36, A:I.56, A:V.60, A:V.60, A:L.64, A:F.66, A:F.66, A:A.74, A:A.78, A:L.112, A:F.118, A:F.118, A:F.118, A:E.193, A:F.196, A:P.197, A:L.200, A:F.201 Hydrogen bonds: A:G.120, A:S.123, A:M.124, A:T.125, A:T.125, A:E.193 Water bridges: A:R.166, A:R.186 Salt bridges: A:R.186 pi-Stacking: A:F.66, A:F.196 Metal complexes: A:C.33 HEM.20: 29 residues within 4Å: Chain B: P.32, C.33, P.34, G.35, L.36, I.56, V.60, L.64, F.66, A.71, A.74, T.75, A.78, L.112, F.118, E.119, G.120, S.123, M.124, T.125, R.186, E.193, F.196, P.197, L.200, F.201, F.220 Ligands: MG.21, MZ0.22 26 PLIP interactions: 26 interactions with chain B, Hydrophobic interactions: B:P.32, B:P.34, B:L.36, B:I.56, B:L.64, B:F.66, B:A.78, B:L.112, B:F.118, B:E.193, B:E.193, B:F.196, B:P.197, B:L.200, B:F.201 Hydrogen bonds: B:E.119, B:G.120, B:M.124, B:T.125, B:T.125 Water bridges: B:R.166, B:E.193 Salt bridges: B:R.186 pi-Stacking: B:F.66, B:F.196 Metal complexes: B:C.33

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 4 residues within 4Å: Chain A: E.119, G.120, S.123 Ligands: HEM.9 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.119, A:G.120, A:S.123, H2O.6, H2O.6 MG.21: 4 residues within 4Å: Chain B: E.119, G.120, S.123 Ligands: HEM.20 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.119, B:G.120, B:S.123, H2O.19, H2O.19

2 x MZ0: 1H-imidazol-5-ylmethanol(Non-covalent)

MZ0.11: 7 residues within 4Å: Chain A: F.66, A.74, F.118, T.189, E.193, F.196 Ligands: HEM.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.189, A:E.193, A:E.193 pi-Stacking: A:F.196 MZ0.22: 7 residues within 4Å: Chain B: F.66, A.74, F.118, T.189, E.193, F.196 Ligands: HEM.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.189 pi-Stacking: B:F.196

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.12: 3 residues within 4Å: Chain A: E.279, N.283, V.319 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.279, A:E.279, A:E.279 NAG.13: 2 residues within 4Å: Chain A: P.291, N.292 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.292 NAG.14: 3 residues within 4Å: Chain A: N.8, S.10 Chain B: E.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.10 NAG.23: 2 residues within 4Å: Chain B: N.8, S.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.8, B:S.10 NAG.25: 5 residues within 4Å: Chain B: N.179, S.181, V.183, D.184, R.254 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.181 Water bridges: B:S.181, B:K.280

2 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.15: 8 residues within 4Å: Chain A: P.2, P.53, V.54, Y.76, D.88, T.303, N.304, F.307 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:P.2, A:D.88, A:N.304 Water bridges: A:D.88, A:D.88, A:D.88, A:D.88 BMA.24: 5 residues within 4Å: Chain B: L.85, I.86, D.88, A.300, T.303 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:I.86, B:D.88, B:K.299 Water bridges: B:I.86, B:T.87, B:N.304, B:N.304, B:N.304

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

SO4.16: 2 residues within 4Å: Chain A: T.294, V.295 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.295 SO4.18: 3 residues within 4Å: Chain A: R.94, T.96, R.97 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.97 Water bridges: A:R.94, A:R.94 Salt bridges: A:R.94, A:R.97 SO4.19: 3 residues within 4Å: Chain A: Y.148, R.151, K.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.148 Salt bridges: A:R.151, A:K.168 SO4.28: 2 residues within 4Å: Chain B: R.94, H.135 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.30, B:R.30, B:N.113 Salt bridges: B:R.94, B:H.135 SO4.30: 4 residues within 4Å: Chain B: K.168 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.144, B:K.168 Salt bridges: B:K.168 SO4.31: 4 residues within 4Å: Chain B: R.94, K.95, T.96, R.97 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.96, B:R.97 Salt bridges: B:R.94, B:R.97

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

CL.17: 6 residues within 4Å: Chain A: P.5, D.67, N.68, P.235 Chain B: S.234, P.235 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain A: P.235 Chain B: P.5, D.67, N.68, P.235 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain B: P.3, G.4 Ligands: TRS.26 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain B: T.140 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4 Ligand excluded by PLIP

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.26: 4 residues within 4Å: Chain B: P.3, E.7, N.58 Ligands: CL.29 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.7, B:N.58 Water bridges: B:N.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Piontek, K. et al., Structural Basis of Substrate Conversion in a New Aromatic Peroxygenase: P450 Functionality with Benefits. J.Biol.Chem. (2013)

Release Date

2013-10-23

Peptides

AROMATIC PEROXYGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

AROMATIC PEROXYGENASE

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