spacer
spacer

PDBsum entry 4igc

Go to PDB code: 
protein metals Protein-protein interface(s) links
Transcription, transferase PDB id
4igc
Jmol PyMol
Contents
Protein chains
323 a.a.
221 a.a.
1335 a.a.
1160 a.a.
90 a.a.
517 a.a.
76 a.a.
458 a.a.
Metals
_MG ×2
_ZN ×4
Superseded by: 4yg2
PDB id:
4igc
Name: Transcription, transferase
Title: X-ray crystal structure of escherichia coli sigma70 holoenzy
Structure: DNA-directed RNA polymerase subunit alpha. Chain: a, b, f, g. Synonym: rnap subunit alpha, RNA polymerase subunit alpha, transcriptase subunit alpha. Engineered: yes. DNA-directed RNA polymerase subunit beta. Chain: c, h. Synonym: rnap subunit beta, RNA polymerase subunit beta, transcriptase subunit beta.
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: rpoa, pez, phs, sez, b3295, jw3257. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rpob, gron, nitb, rif, ron, stl, stv, tabd, b3987, jw gene: rpoc, tabb, b3988, jw3951. Organism_taxid: 1110693.
Resolution:
3.70Å     R-factor:   0.244     R-free:   0.285
Authors: K.S.Murakami
Key ref: K.S.Murakami (2013). X-ray crystal structure of Escherichia coli RNA polymerase σ70 holoenzyme. J Biol Chem, 288, 9126-9134. PubMed id: 23389035 DOI: 10.1074/jbc.M112.430900
Date:
17-Dec-12     Release date:   06-Feb-13    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A7Z4  (RPOA_ECOLI) -  DNA-directed RNA polymerase subunit alpha
Seq:
Struc:
329 a.a.
323 a.a.
Protein chains
Pfam   ArchSchema ?
P0A7Z4  (RPOA_ECOLI) -  DNA-directed RNA polymerase subunit alpha
Seq:
Struc:
329 a.a.
221 a.a.
Protein chains
Pfam   ArchSchema ?
P0A8V2  (RPOB_ECOLI) -  DNA-directed RNA polymerase subunit beta
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1342 a.a.
1335 a.a.
Protein chains
Pfam   ArchSchema ?
P0A8T7  (RPOC_ECOLI) -  DNA-directed RNA polymerase subunit beta'
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1407 a.a.
1160 a.a.
Protein chain
Pfam   ArchSchema ?
H0QDQ9  (H0QDQ9_ECOLI) -  DNA-directed RNA polymerase subunit omega
Seq:
Struc:
91 a.a.
90 a.a.
Protein chain
Pfam   ArchSchema ?
P00579  (RPOD_ECOLI) -  RNA polymerase sigma factor RpoD
Seq:
Struc:
 
Seq:
Struc:
613 a.a.
517 a.a.
Protein chain
Pfam   ArchSchema ?
H0QDQ9  (H0QDQ9_ECOLI) -  DNA-directed RNA polymerase subunit omega
Seq:
Struc:
91 a.a.
76 a.a.
Protein chain
Pfam   ArchSchema ?
P00579  (RPOD_ECOLI) -  RNA polymerase sigma factor RpoD
Seq:
Struc:
 
Seq:
Struc:
613 a.a.
458 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, C, D, E, H, I: E.C.2.7.7.6  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M112.430900 J Biol Chem 288:9126-9134 (2013)
PubMed id: 23389035  
 
 
X-ray crystal structure of Escherichia coli RNA polymerase σ70 holoenzyme.
K.S.Murakami.
 
  ABSTRACT  
 
Escherichia coli RNA polymerase (RNAP) is the most studied bacterial RNAP and has been used as the model RNAP for screening and evaluating potential RNAP-targeting antibiotics. However, the x-ray crystal structure of E. coli RNAP has been limited to individual domains. Here, I report the x-ray structure of the E. coli RNAP σ(70) holoenzyme, which shows σ region 1.1 (σ1.1) and the α subunit C-terminal domain for the first time in the context of an intact RNAP. σ1.1 is positioned at the RNAP DNA-binding channel and completely blocks DNA entry to the RNAP active site. The structure reveals that σ1.1 contains a basic patch on its surface, which may play an important role in DNA interaction to facilitate open promoter complex formation. The α subunit C-terminal domain is positioned next to σ domain 4 with a fully stretched linker between the N- and C-terminal domains. E. coli RNAP crystals can be prepared from a convenient overexpression system, allowing further structural studies of bacterial RNAP mutants, including functionally deficient and antibiotic-resistant RNAPs.
 

 

spacer

spacer