SMTL ID : 6ow3.1

X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter variant -1T

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

hetero-2-1-1-1-1-mer

Ligands

1 x GTP- G- G- G: RNA (5'-D(*(GTP))-R(P*GP*GP*G)-3')(Non-covalent)

GTP-G-G-G.1: 25 residues within 4Å: Chain C: Q.390, R.409, L.413, R.420, P.444, N.448, I.452, Q.567, K.838, K.846, H.999 Chain D: R.704, A.705, P.706, D.739, D.741, D.743 Chain F: D.323, E.324 Chain G: C.13, C.14, C.15, T.16, A.17 Ligands: MG.4 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain F Hydrogen bonds: C:Q.390, C:R.409, C:R.409, C:N.448, C:N.448, F:D.323, F:D.323, F:D.323, F:D.323, F:E.324 Salt bridges: C:R.420

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: E.154 Chain D: L.839, K.840 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Metal complexes: B:E.154, D:K.840 MG.4: 4 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: GTP-G-G-G.1 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.739, D:D.741, D:D.741, D:D.743, D:D.743

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.3: 3 residues within 4Å: Chain C: R.879 Chain D: D.739, R.1029 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:R.879, D:R.1029

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain D: C.58, C.60, C.73, C.76 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.58, D:C.60, D:C.73, D:C.76 ZN.6: 6 residues within 4Å: Chain D: C.1112, T.1114, C.1194, Q.1195, C.1201, C.1204 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.1112, D:C.1194, D:C.1201, D:C.1204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, Y. et al., Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase. Nucleic Acids Res. (2020)

Release Date

2019-07-24

Peptides

DNA-directed RNA polymerase subunit alpha: AB
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit beta': D
DNA-directed RNA polymerase subunit omega: E
RNA polymerase sigma factor SigA: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

RNA polymerase sigma factor SigA

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