SMTL ID : 2v4j.1

THE CRYSTAL STRUCTURE OF Desulfovibrio vulgaris DISSIMILATORY SULFITE REDUCTASE BOUND TO DsrC PROVIDES NOVEL INSIGHTS INTO THE MECHANISM OF SULFATE RESPIRATION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-2-mer

Ligands

8 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 11 residues within 4Å: Chain A: C.177, L.178, C.183, F.185, A.186, A.220, C.221, N.223, G.224, C.225 Ligands: SH0.3 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:D.219 Metal complexes: A:C.177, A:C.183, A:C.221, A:C.225 SF4.2: 11 residues within 4Å: Chain A: C.284, P.285, C.288, M.289, C.303, V.304, R.305, C.306, M.307, H.308, C.309 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.284, A:C.303, A:C.306, A:C.309 SF4.4: 11 residues within 4Å: Chain B: T.145, Q.146, C.151, T.153, P.154, A.187, C.188, C.189, N.191, C.193 Ligands: SRM.6 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.151, B:C.188, B:C.189, B:C.193 SF4.5: 13 residues within 4Å: Chain B: P.211, S.230, C.231, P.232, T.233, V.236, I.253, C.258, M.259, Y.260, C.261, G.262, C.264 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.231, B:C.258, B:C.261, B:C.264 SF4.8: 12 residues within 4Å: Chain D: C.177, L.178, C.183, F.185, A.186, D.219, A.220, C.221, N.223, G.224, C.225 Ligands: SH0.10 5 PLIP interactions: 5 interactions with chain D, Salt bridges: D:D.219 Metal complexes: D:C.177, D:C.183, D:C.221, D:C.225 SF4.9: 11 residues within 4Å: Chain D: C.284, P.285, C.288, M.289, C.303, V.304, R.305, C.306, M.307, H.308, C.309 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.284, D:C.303, D:C.306, D:C.309 SF4.11: 11 residues within 4Å: Chain E: T.145, Q.146, C.151, T.153, P.154, A.187, C.188, C.189, N.191, C.193 Ligands: SRM.13 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.151, E:C.188, E:C.189, E:C.193 SF4.12: 13 residues within 4Å: Chain E: P.211, S.230, C.231, P.232, T.233, V.236, I.253, C.258, M.259, Y.260, C.261, G.262, C.264 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.231, E:C.258, E:C.261, E:C.264

2 x SH0: 3,3',3'',3'''-[(1R,2S,3S,4S,7S,8S,11S,12S,13S,16S,19S)-3,8,13,17-tetrakis(carboxylatomethyl)-8,13-dimethyl-1,2,3,4,7,8,11,12,13,16,19,20,22,24-tetradecahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoate(Non-covalent)

SH0.3: 33 residues within 4Å: Chain A: C.177, L.178, R.182, C.183, E.184, F.185, N.223, G.224, C.225, N.262, N.311 Chain B: H.44, I.46, H.54, R.66, R.94, T.96, T.97, R.98, N.100, E.102, G.134, T.135, G.136, S.140, P.181, R.183, K.288, V.289, S.290, R.292, R.336 Ligands: SF4.1 40 PLIP interactions: 7 interactions with chain A, 33 interactions with chain B Hydrophobic interactions: A:L.178, A:N.311, B:T.96, B:R.98, B:V.289 Hydrogen bonds: A:L.178, A:N.262, A:N.311, B:T.96, B:T.97, B:N.100, B:G.136, B:S.140, B:R.183, B:V.289, B:S.290, B:S.290, B:S.290 Water bridges: A:R.231, A:R.231, B:R.94, B:R.94, B:R.98, B:R.98, B:R.183, B:R.292, B:R.292, B:R.292, B:R.336 Salt bridges: B:H.44, B:H.54, B:R.66, B:R.66, B:R.94, B:R.98, B:R.183, B:R.292, B:R.292, B:R.336, B:R.336 SH0.10: 33 residues within 4Å: Chain D: C.177, L.178, R.182, C.183, E.184, F.185, N.223, G.224, C.225, N.262, N.311 Chain E: H.44, L.52, H.54, R.66, R.94, T.96, T.97, R.98, N.100, E.102, G.134, T.135, G.136, S.140, P.181, R.183, K.288, V.289, S.290, R.292, R.336 Ligands: SF4.8 39 PLIP interactions: 32 interactions with chain E, 7 interactions with chain D Hydrophobic interactions: E:T.96, E:R.98, E:V.289, D:L.178, D:N.223, D:N.311 Hydrogen bonds: E:T.96, E:T.97, E:N.100, E:G.136, E:S.140, E:R.183, E:V.289, E:S.290, E:S.290, E:S.290, D:L.178, D:N.262, D:N.311 Water bridges: E:R.94, E:R.94, E:R.98, E:R.98, E:K.288, E:R.292, E:R.292, E:R.292, D:R.231 Salt bridges: E:H.44, E:H.54, E:R.66, E:R.66, E:R.94, E:R.98, E:R.183, E:R.292, E:R.292, E:R.336, E:R.336

2 x SRM: SIROHEME(Non-covalent)

SRM.6: 33 residues within 4Å: Chain A: I.81, R.83, R.101, G.134, S.135, T.136, G.137, D.138, Y.212, K.213, K.215, K.217, R.231, K.332, A.333, I.335, R.376, R.378 Chain B: R.71, H.144, T.145, Q.146, H.150, C.151, H.152, N.191, M.192, C.193, G.194 Chain C: G.103, C.104 Ligands: SF4.4, SO3.7 44 PLIP interactions: 10 interactions with chain B, 33 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: B:T.145, B:Q.146, B:N.191, A:A.333 Water bridges: B:Q.146, B:N.191, B:T.266, A:R.83, A:R.83, A:R.101, A:R.101, A:T.136, A:I.335, A:R.378, A:R.378 Salt bridges: B:R.71, B:H.150, B:H.152, A:R.83, A:R.83, A:R.101, A:K.213, A:K.213, A:K.215, A:K.215, A:K.217, A:R.231, A:K.332, A:R.376, A:R.378, A:R.378 Metal complexes: B:C.193 Hydrogen bonds: A:G.134, A:S.135, A:S.135, A:T.136, A:G.137, A:D.138, A:D.138, A:Y.212, A:A.333, C:C.104 pi-Cation interactions: A:K.213, A:K.215 SRM.13: 33 residues within 4Å: Chain D: I.81, R.83, R.101, G.134, S.135, T.136, G.137, D.138, Y.212, K.213, K.215, K.217, R.231, K.332, A.333, I.335, R.376, R.378 Chain E: R.71, H.144, T.145, Q.146, H.150, C.151, H.152, N.191, M.192, C.193, G.194 Chain F: G.103, C.104 Ligands: SF4.11, SO3.14 40 PLIP interactions: 10 interactions with chain E, 29 interactions with chain D, 1 interactions with chain F, Hydrophobic interactions: E:T.145, E:Q.146, E:N.191 Water bridges: E:Q.146, E:N.191, E:T.266, D:R.83, D:R.101, D:T.136, D:I.335, D:L.336, D:R.378, D:R.378 Salt bridges: E:R.71, E:H.150, E:H.152, D:R.83, D:R.83, D:R.101, D:K.213, D:K.213, D:K.215, D:K.215, D:K.217, D:R.231, D:K.332, D:R.376, D:R.378, D:R.378 Metal complexes: E:C.193 Hydrogen bonds: D:G.134, D:S.135, D:S.135, D:T.136, D:G.137, D:D.138, D:A.333, F:C.104 pi-Cation interactions: D:K.213, D:K.215

2 x SO3: SULFITE ION(Non-covalent)

SO3.7: 6 residues within 4Å: Chain A: R.101, R.172, K.213, K.215 Chain C: C.104 Ligands: SRM.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.101, A:R.101, A:R.172, A:R.172, A:K.213, A:K.215 Water bridges: A:T.136, A:T.136, A:R.172 SO3.14: 6 residues within 4Å: Chain D: R.101, R.172, K.213, K.215 Chain F: C.104 Ligands: SRM.13 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:R.101, D:R.101, D:R.172, D:R.172, D:K.213, D:K.213, D:K.215 Water bridges: D:T.136, D:T.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oliveira, T.F. et al., The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration. J.Biol.Chem. (2008)

Release Date

2008-12-02

Peptides

SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT ALPHA: AD
SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT BETA: BE
SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT GAMMA: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT ALPHA

SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT BETA

SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT GAMMA