SMTL ID : 4r3u.2 (1 other biounit)

Crystal structure of 2-Hydroxyisobutyryl-CoA Mutase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 x 3HC: 3-HYDROXYBUTANOYL-COENZYME A(Non-covalent)

3HC.1: 33 residues within 4Å: Chain A: Y.87, T.89, M.90, S.93, R.94, T.97, R.99, I.101, S.126, D.128, S.176, T.178, T.207, Q.209, Q.219, R.246, N.248, N.251, Y.255, H.256, R.295, A.297, F.299, R.339, F.340, H.341, Q.343, Q.374, S.375 Chain C: F.38, A.42 Ligands: 3KK.2, B12.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.255, A:F.299, A:H.341 Hydrogen bonds: A:Y.87, A:Y.87, A:T.89, A:S.93, A:R.94, A:R.94, A:T.97, A:S.176, A:Q.209, A:N.251, A:N.251, A:R.339, A:Q.343, A:S.375 Water bridges: A:R.94 Salt bridges: A:R.99, A:R.246, A:R.295 3HC.4: 33 residues within 4Å: Chain A: F.38, A.42 Chain C: Y.87, T.89, M.90, S.93, R.94, T.97, R.99, I.101, S.126, D.128, S.176, T.178, T.207, Q.209, Q.219, R.246, N.248, N.251, Y.255, H.256, R.295, A.297, F.299, R.339, F.340, H.341, Q.343, Q.374, S.375 Ligands: 3KK.5, B12.6 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:Y.255, C:F.299, C:H.341 Hydrogen bonds: C:Y.87, C:T.89, C:T.89, C:S.93, C:R.94, C:R.94, C:T.97, C:S.176, C:T.207, C:Q.209, C:N.251, C:N.251, C:R.339, C:Q.343, C:S.375 Water bridges: C:R.94 Salt bridges: C:R.99, C:R.246, C:R.295

2 x 3KK: S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} 2-hydroxy-2-methylpropanethioate(Non-covalent)

3KK.2: 33 residues within 4Å: Chain A: Y.87, T.89, M.90, S.93, R.94, T.97, R.99, I.101, S.126, D.128, S.176, T.178, T.207, Q.209, Q.219, R.246, N.248, N.251, Y.255, H.256, R.295, A.297, F.299, R.339, F.340, H.341, Q.343, Q.374, S.375 Chain C: F.38, A.42 Ligands: 3HC.1, B12.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:T.178, A:Y.255, A:H.341 Hydrogen bonds: A:Y.87, A:T.89, A:S.93, A:R.94, A:R.94, A:T.97, A:S.176, A:T.207, A:Q.209, A:N.251, A:N.251, A:R.339, A:S.375 Water bridges: A:R.94 Salt bridges: A:R.99, A:R.246, A:R.295 3KK.5: 33 residues within 4Å: Chain A: F.38, A.42 Chain C: Y.87, T.89, M.90, S.93, R.94, T.97, R.99, I.101, S.126, D.128, S.176, T.178, T.207, Q.209, Q.219, R.246, N.248, N.251, Y.255, H.256, R.295, A.297, F.299, R.339, F.340, H.341, Q.343, Q.374, S.375 Ligands: 3HC.4, B12.6 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:T.178, C:Y.255, C:H.341 Hydrogen bonds: C:T.89, C:T.89, C:S.93, C:R.94, C:R.94, C:T.97, C:S.176, C:T.207, C:T.207, C:Q.209, C:N.251, C:N.251, C:R.339, C:S.375 Water bridges: C:R.94 Salt bridges: C:R.99, C:R.246, C:R.295

2 x B12: COBALAMIN(Non-covalent)

B12.3: 43 residues within 4Å: Chain A: D.128, F.129, M.131, L.134, E.151, A.218, Q.219, E.221, Y.255, H.256, E.259, A.260, A.346, A.347, E.383, A.384, F.385, A.386, I.387 Chain B: D.27, G.28, H.29, D.30, R.31, G.32, V.36, G.72, V.73, S.74, L.76, S.77, G.78, I.102, A.103, G.104, G.105, L.124, L.125, Q.126, T.128, I.133 Ligands: 3HC.1, 3KK.2 28 PLIP interactions: 17 interactions with chain B, 11 interactions with chain A, Hydrophobic interactions: B:V.36, B:I.102, B:I.102, B:I.133, A:Q.219, A:Y.255, A:H.256, A:A.260, A:A.346, A:I.387 Hydrogen bonds: B:G.28, B:H.29, B:D.30, B:D.30, B:R.31, B:G.32, B:L.76, B:G.105, B:G.105, B:Q.126, B:Q.126, B:D.127, A:D.128, A:F.129, A:E.151, A:E.221, A:E.383 Metal complexes: B:H.29 B12.6: 43 residues within 4Å: Chain C: D.128, F.129, M.131, L.134, E.151, A.218, Q.219, E.221, Y.255, H.256, E.259, A.260, A.346, A.347, E.383, A.384, F.385, A.386, I.387 Chain D: D.27, G.28, H.29, D.30, R.31, G.32, V.36, G.72, V.73, S.74, L.76, S.77, G.78, I.102, A.103, G.104, G.105, L.124, L.125, Q.126, T.128, I.133 Ligands: 3HC.4, 3KK.5 30 PLIP interactions: 11 interactions with chain C, 19 interactions with chain D, Hydrophobic interactions: C:Q.219, C:Y.255, C:H.256, C:A.260, C:A.346, C:I.387, D:V.36, D:I.102, D:I.102, D:I.133 Hydrogen bonds: C:F.129, C:E.151, C:E.221, C:E.221, C:E.383, D:D.27, D:G.28, D:H.29, D:D.30, D:D.30, D:D.30, D:R.31, D:G.32, D:L.76, D:G.105, D:G.105, D:Q.126, D:Q.126, D:D.127 Metal complexes: D:H.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kurteva-Yaneva, N. et al., Structural basis of the stereospecificity of bacterial B12-dependent 2-hydroxyisobutyryl-CoA mutase. J.Biol.Chem. (2015)

Release Date

2015-03-11

Peptides

2-hydroxyisobutyryl-CoA mutase large subunit: AC
2-hydroxyisobutyryl-CoA mutase small subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
B

B
D

D
D

2-hydroxyisobutyryl-CoA mutase large subunit

2-hydroxyisobutyryl-CoA mutase small subunit

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