SMTL ID : 4q73.1

Crystal Structure of Bradyrhizobium japonicum Proline Utilization A (PutA) Mutant D778Y

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 27 residues within 4Å: Chain A: D.280, A.281, A.312, Q.314, Y.316, R.341, V.343, K.344, G.345, A.346, Y.347, W.348, F.366, T.367, R.368, K.369, T.372, A.395, T.396, H.397, N.398, Q.418, R.419, Y.443, S.467, S.468, F.469 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:A.395, A:Y.443 Hydrogen bonds: A:A.281, A:A.281, A:Q.314, A:R.341, A:K.344, A:G.345, A:G.345, A:G.345, A:A.346, A:T.367, A:T.372, A:D.373, A:T.396, A:H.397, A:H.397, A:N.398, A:N.398, A:S.467, A:F.469 Salt bridges: A:K.344, A:K.344, A:K.369 Water bridges: A:K.369, A:V.470 pi-Stacking: A:W.348, A:W.348 FAD.8: 26 residues within 4Å: Chain B: D.280, A.281, A.312, Q.314, Y.316, R.341, V.343, K.344, G.345, A.346, Y.347, W.348, F.366, T.367, R.368, K.369, T.372, A.395, T.396, H.397, N.398, R.419, Y.443, S.467, S.468, F.469 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:A.395, B:Y.443 Hydrogen bonds: B:A.281, B:A.281, B:Q.314, B:R.341, B:K.344, B:G.345, B:G.345, B:G.345, B:A.346, B:T.367, B:K.369, B:H.397, B:H.397, B:N.398, B:N.398, B:S.467, B:F.469 Salt bridges: B:K.344, B:K.344, B:K.369 pi-Stacking: B:W.348, B:W.348 FAD.15: 27 residues within 4Å: Chain C: D.280, A.281, A.312, Q.314, Y.316, R.341, V.343, K.344, G.345, A.346, Y.347, W.348, F.366, T.367, R.368, K.369, T.372, A.395, T.396, H.397, N.398, Q.418, R.419, Y.443, S.467, S.468, F.469 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:A.395, C:Y.443 Hydrogen bonds: C:A.281, C:A.281, C:Q.314, C:R.341, C:K.344, C:G.345, C:G.345, C:G.345, C:A.346, C:T.367, C:D.373, C:H.397, C:H.397, C:N.398, C:N.398, C:S.467, C:F.469 Salt bridges: C:K.344, C:K.344, C:K.369 Water bridges: C:K.369, C:V.470 pi-Stacking: C:W.348, C:W.348 FAD.22: 26 residues within 4Å: Chain D: D.280, A.281, A.312, Q.314, Y.316, R.341, V.343, K.344, G.345, A.346, Y.347, W.348, F.366, T.367, R.368, K.369, T.372, A.395, T.396, H.397, N.398, R.419, Y.443, S.467, S.468, F.469 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:A.395, D:Y.443 Hydrogen bonds: D:A.281, D:A.281, D:Q.314, D:R.341, D:K.344, D:G.345, D:G.345, D:G.345, D:A.346, D:T.367, D:K.369, D:T.372, D:T.396, D:H.397, D:H.397, D:N.398, D:N.398, D:S.467, D:F.469 Salt bridges: D:K.344, D:K.344, D:K.369 pi-Stacking: D:W.348, D:W.348

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

SO4.2: 8 residues within 4Å: Chain A: F.661, R.793, C.794, S.795, I.947, G.948, A.949, F.956 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: G.572, R.626 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.368, K.369, A.370 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: L.584, S.587, R.588 Ligand excluded by PLIP SO4.9: 7 residues within 4Å: Chain B: F.661, R.793, S.795, I.947, G.948, A.949, F.956 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain B: G.572, R.626 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain B: R.368, K.369, A.370 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: L.584, S.587, R.588 Ligand excluded by PLIP SO4.16: 8 residues within 4Å: Chain C: F.661, R.793, C.794, S.795, I.947, G.948, A.949, F.956 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain C: G.572, R.626 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain C: R.368, K.369, A.370 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain C: L.584, S.587, R.588 Ligand excluded by PLIP SO4.23: 7 residues within 4Å: Chain D: F.661, R.793, S.795, I.947, G.948, A.949, F.956 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain D: G.572, R.626 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain D: R.368, K.369, A.370 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain D: L.584, S.587, R.588 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: Y.14, A.15, L.360, D.361, V.519, E.520, A.526 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.361, A:E.520 GOL.7: 5 residues within 4Å: Chain A: R.358, V.519, E.520, F.521, D.605 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.358, A:V.519, A:F.521, A:D.605 GOL.13: 6 residues within 4Å: Chain B: Y.14, L.360, D.361, V.519, E.520, A.526 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.361, B:E.520 GOL.14: 4 residues within 4Å: Chain B: R.358, V.519, E.520, F.521 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.520, B:F.521 GOL.20: 7 residues within 4Å: Chain C: Y.14, A.15, L.360, D.361, V.519, E.520, A.526 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.361, C:E.520 GOL.21: 5 residues within 4Å: Chain C: R.358, V.519, E.520, F.521, D.605 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.358, C:V.519, C:F.521, C:D.605 GOL.27: 6 residues within 4Å: Chain D: Y.14, L.360, D.361, V.519, E.520, A.526 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.361, D:E.520 GOL.28: 4 residues within 4Å: Chain D: R.358, V.519, E.520, F.521 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.520, D:F.521

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Arentson, B.W. et al., Kinetic and Structural Characterization of Tunnel-Perturbing Mutants in Bradyrhizobium japonicum Proline Utilization A. Biochemistry (2014)

Peptides

Proline dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Proline dehydrogenase