Brand  (β version)

PDB ID: 4OIQ

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Ligands
Code Name Style Show Link
MB8 (2z)-2-methylbut-2-enoic acid PoSSuM
MG Magnesium ion PoSSuM
ZN Zinc ion PoSSuM
Non-standard Residues
Code Name Show
0QZ D-isoserine
2RA 3-amino-D-alanine
2TL D-allothreonine
DSN D-serine
DVA D-valine
FGL 2-aminopropanedioic acid
R2T Beta,gamma-dihydroxyglutamine
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 4OIQ   PDBj   RCSB PDB   PDBe
Header : TRANSCRIPTION, TRANSFERASE/ANTIBIOTIC
Title : Crystal structure of Thermus thermophilus transcription initiation complex soaked with GE23077 and rifampicin
Release Data : 2014-05-07
Compound :
mol_id molecule chains synonym
1 DNA-directed RNA polymerase subunit alpha A,B RNAP subunit alpha, RNA polymerase subunit alpha, Transcriptase subunit alpha
ec: 2.7.7.6
mol_id molecule chains synonym
2 DNA-directed RNA polymerase subunit beta C RNAP subunit beta, RNA polymerase subunit beta, Transcriptase subunit beta
ec: 2.7.7.6
mol_id molecule chains synonym
3 DNA-directed RNA polymerase subunit beta' D RNAP subunit beta', RNA polymerase subunit beta', Transcriptase subunit beta'
ec: 2.7.7.6
mol_id molecule chains synonym
4 DNA-directed RNA polymerase subunit omega E RNAP omega subunit, RNA polymerase omega subunit, Transcriptase subunit omega
ec: 2.7.7.6
mol_id molecule chains synonym
5 DNA directed RNA polymerase sigma factor A F RNA polymerase sigma factor
mol_id molecule chains
6 5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3' G
other_details: promoter DNA template strand
mol_id molecule chains
7 5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3' H
other_details: promoter DNA nontemplate strand
mol_id molecule chains
8 GE23077 I
Source :
mol_id organism_scientific
1 Thermus thermophilus  (taxid:300852)
strain: HB8 / ATCC 27634 / DSM 579
mol_id organism_scientific
2 Thermus thermophilus  (taxid:300852)
strain: HB8 / ATCC 27634 / DSM 579
mol_id organism_scientific
3 Thermus thermophilus  (taxid:300852)
strain: HB8 / ATCC 27634 / DSM 579
mol_id organism_scientific
4 Thermus thermophilus  (taxid:300852)
strain: HB8 / ATCC 27634 / DSM 579
mol_id organism_scientific expression_system
5 Thermus thermophilus  (taxid:300852) Escherichia coli  (taxid:469008)
strain: HB8 / ATCC 27634 / DSM 579
gene: rpoD, TTHA0532
expression_system_strain: BL21(DE3)
expression_system_vector_type: plasmid
expression_system_plasmid: pET28a
mol_id organism_scientific
6
synthetic: yes
mol_id organism_scientific
7
synthetic: yes
mol_id organism_scientific
8 Actinomadura sp.  (taxid:1989)
synthetic: yes
Authors : Zhang, Y., Ebright, R.H., Arnold, E.
Keywords : GE23077, transcription inhibitor, transcription open complex, transcription initiation complex, i site, i+1 site, rifampicin, Rif, Rifampin, RNA polymerase, DNA/RNA/NTP binding, polymerization of ribonucleotides, nucleoid, TRANSCRIPTION, TRANSFERASE-ANTIBIOTIC complex
Exp. method : X-RAY DIFFRACTION ( 3.624 Å )
Citation :

GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.

Zhang, Y.,Degen, D.,Ho, M.X.  et al.
(2014)  Elife  3 : e02450 - e02450

PubMed: 24755292

Reaction

Chain : A, B
UniProt : Q5SHR6 (RPOA_THET8)
Reaction: EC: Evidence:
Physiological Direction:
RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate 2.7.7.6 -
-
Chain : C
UniProt : Q8RQE9 (RPOB_THET8)
Reaction: EC: Evidence:
Physiological Direction:
RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate 2.7.7.6 HAMAP-Rule:MF_01321
-
Chain : D
UniProt : Q8RQE8 (RPOC_THET8)
Reaction: EC: Evidence:
Physiological Direction:
RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate 2.7.7.6 HAMAP-Rule:MF_01322
-
Cofactor: Evidence: Note:
Mg(2+) ECO:0000255 | HAMAP-Rule:MF_01322
Binds 1 Mg(2+) ion per subunit.
Zn(2+) ECO:0000255 | HAMAP-Rule:MF_01322
Binds 2 Zn(2+) ions per subunit.
Chain : E
UniProt : Q8RQE7 (RPOZ_THET8)
Reaction: EC: Evidence:
Physiological Direction:
RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate 2.7.7.6 HAMAP-Rule:MF_00366
-
Chain : F
UniProt : Q5SKW1 (Q5SKW1_THET8)
Reaction : -