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PDBsum entry 4b1p

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protein dna_rna ligands metals Protein-protein interface(s) links
Transferase/DNA PDB id
4b1p
Jmol
Contents
Protein chains
84 a.a.
49 a.a.
91 a.a.
65 a.a.
1103 a.a.
262 a.a.
171 a.a.
105 a.a.
113 a.a.
872 a.a.
44 a.a.
376 a.a.
76 a.a.
DNA/RNA
Ligands
SF4
Metals
_ZN ×6
_MG
PDB id:
4b1p
Name: Transferase/DNA
Title: Archaeal rnap-DNA binary complex at 4.32ang
Structure: 5'-d( Tp Cp Tp Tp Ap Tp Ap Cp Tp Cp Tp Ap Tp Cp)- chain: c. 5'-d( Ap Tp Ap Gp Ap Gp Tp Ap Tp Ap Ap Gp Ap Tp Chain: d. DNA-directed RNA polymerase subunit k. Chain: i. Other_details: rpo6. RNA polymerase subunit 13. Chain: j.
Source: Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Sulfolobus shibatae b12. Organism_taxid: 523848. Organism_taxid: 523848
Resolution:
4.32Å     R-factor:   0.292     R-free:   0.310
Authors: M.N.Wojtas,M.Mogni,O.Millet,S.D.Bell,N.G.A.Abrescia
Key ref: M.N.Wojtas et al. (2012). Structural and functional analyses of the interaction of archaeal RNA polymerase with DNA. Nucleic Acids Res, 40, 9941-9952. PubMed id: 22848102 DOI: 10.1093/nar/gks692
Date:
12-Jul-12     Release date:   08-Aug-12    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
B8YB61  (B8YB61_SULSH) -  DNA-directed RNA polymerase subunit K
Seq:
Struc:
95 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB65  (B8YB65_SULSH) -  RNA polymerase subunit 13
Seq:
Struc:
104 a.a.
49 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB62  (B8YB62_SULSH) -  DNA-directed RNA polymerase subunit L
Seq:
Struc:
92 a.a.
91 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB63  (B8YB63_SULSH) -  DNA-directed RNA polymerase subunit N
Seq:
Struc:
66 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB55  (B8YB55_SULSH) -  DNA-directed RNA polymerase
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1131 a.a.
1103 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB56  (B8YB56_SULSH) -  DNA-directed RNA polymerase subunit D
Seq:
Struc:
265 a.a.
262 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB57  (B8YB57_SULSH) -  RNA polymerase subunit 7
Seq:
Struc:
180 a.a.
171 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB58  (B8YB58_SULSH) -  RNA polymerase subunit 4
Seq:
Struc:
113 a.a.
105 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB59  (B8YB59_SULSH) -  RNA polymerase subunit 8
Seq:
Struc:
132 a.a.
113 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB53  (B8YB53_SULSH) -  DNA-directed RNA polymerase
Seq:
Struc:
 
Seq:
Struc:
880 a.a.
872 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB64  (B8YB64_SULSH) -  DNA-directed RNA polymerase subunit P
Seq:
Struc:
48 a.a.
44 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB54  (B8YB54_SULSH) -  DNA-directed RNA polymerase subunit A''
Seq:
Struc:
395 a.a.
376 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB60  (B8YB60_SULSH) -  DNA-directed RNA polymerase subunit H
Seq:
Struc:
84 a.a.
76 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure

 Enzyme reactions 
   Enzyme class: Chains I, M, O, R, S, W, X, Y, Z: 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
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     cellular metabolic process   2 terms 
  Biochemical function     catalytic activity     15 terms  

 

 
    reference    
 
 
DOI no: 10.1093/nar/gks692 Nucleic Acids Res 40:9941-9952 (2012)
PubMed id: 22848102  
 
 
Structural and functional analyses of the interaction of archaeal RNA polymerase with DNA.
M.N.Wojtas, M.Mogni, O.Millet, S.D.Bell, N.G.Abrescia.
 
  ABSTRACT  
 
Multi-subunit RNA polymerases (RNAPs) in all three domains of life share a common ancestry. The composition of the archaeal RNAP (aRNAP) is not identical between phyla and species, with subunits Rpo8 and Rpo13 found in restricted subsets of archaea. While Rpo8 has an ortholog, Rpb8, in the nuclear eukaryal RNAPs, Rpo13 lacks clear eukaryal orthologs. Here, we report crystal structures of the DNA-bound and free form of the aRNAP from Sulfolobus shibatae. Together with biochemical and biophysical analyses, these data show that Rpo13 C-terminus binds non-specifically to double-stranded DNA. These interactions map on our RNAP-DNA binary complex on the downstream DNA at the far end of the DNA entry channel. Our findings thus support Rpo13 as a RNAP-DNA stabilization factor, a role reminiscent of eukaryotic general transcriptional factors. The data further yield insight into the mechanisms and evolution of RNAP-DNA interaction.