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PDBsum entry 4ayb

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
4ayb
Jmol
Contents
Protein chains
872 a.a.
1103 a.a.
376 a.a.
262 a.a.
171 a.a.
105 a.a.
113 a.a.
76 a.a.
84 a.a.
91 a.a.
65 a.a.
44 a.a.
50 a.a.
Ligands
SF4
Metals
_MG
_ZN ×10
PDB id:
4ayb
Name: Transferase
Title: Rnap at 3.2ang
Structure: DNA-directed RNA polymerase. Chain: a. Other_details: rpo1n subunit. DNA-directed RNA polymerase. Chain: b. Other_details: rpo2. DNA-directed RNA polymerase. Chain: c. Other_details: rpo1c.
Source: Sulfolobus shibatae. Archaea. Organism_taxid: 2286. Organism_taxid: 2286
Resolution:
3.20Å     R-factor:   0.245     R-free:   0.300
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
Date:
19-Jun-12     Release date:   08-Aug-12    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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 ?
B8YB55  (B8YB55_SULSH) -  DNA-directed RNA polymerase
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1131 a.a.
1103 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 ?
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 ?
B8YB60  (B8YB60_SULSH) -  DNA-directed RNA polymerase subunit H
Seq:
Struc:
84 a.a.
76 a.a.
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 ?
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 ?
B8YB64  (B8YB64_SULSH) -  DNA-directed RNA polymerase subunit P
Seq:
Struc:
48 a.a.
44 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB65  (B8YB65_SULSH) -  RNA polymerase subunit 13
Seq:
Struc:
104 a.a.
50 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, H, K, L, N, P: 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     14 terms  

 

 
    reference    
 
 
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.