SMTL ID : 6p71.1

X-ray crystal structure of a bacterial reiterative transcription complex of pyrBI promoter

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.92 Å

Oligo State

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

Ligands

1 x A- A- U- U: RNA (5'-R(P*AP*AP*UP*U)-3')(Non-covalent)

A-A-U-U.1: 22 residues within 4Å: Chain C: R.409, R.420, P.444, N.448, Q.567, K.838, K.846, H.999 Chain D: R.704, A.705, D.739, D.741, G.742, D.743 Chain F: D.323 Chain G: A.11, A.12, T.13, T.14, G.15 Ligands: MG.2, UTP.6 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: A-A-U-U.1, UTP.6 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.739, D:D.739, D:D.741, D:D.741, D:D.743 MG.3: 4 residues within 4Å: Chain C: D.686, R.879 Chain D: D.739 Ligands: UTP.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.739

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain D: C.1112, C.1194, 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 ZN.5: 5 residues within 4Å: Chain D: C.58, C.60, G.61, 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

1 x UTP: URIDINE 5'-TRIPHOSPHATE(Covalent)

UTP.6: 17 residues within 4Å: Chain C: S.878, R.879 Chain D: R.704, P.706, N.737, D.739, D.741, R.1029, Q.1235, M.1238, R.1239, H.1242 Chain G: A.10, A.11 Ligands: A-A-U-U.1, MG.2, MG.3 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.704, D:R.704, D:N.737, D:D.741, D:Q.1235, D:R.1239, C:S.878 Salt bridges: D:R.1029, D:H.1242, D:H.1242, C:R.879

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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