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PDBsum entry 3qt1

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protein metals Protein-protein interface(s) links
Transferase, transcription PDB id
3qt1
Jmol
Contents
Protein chains
1416 a.a.
1103 a.a.
266 a.a.
178 a.a.
214 a.a.
87 a.a.
171 a.a.
134 a.a.
47 a.a.
65 a.a.
114 a.a.
46 a.a.
Metals
_MG
_ZN ×7
PDB id:
3qt1
Name: Transferase, transcription
Title: RNA polymerase ii variant containing a chimeric rpb9-c11 sub
Structure: DNA-directed RNA polymerase ii subunit rpb1. Chain: a. Synonym: rpb1, RNA polymerase ii subunit 1, RNA polymerase b1, DNA-directed RNA polymerase iii largest subunit, RNA po ii subunit b220. DNA-directed RNA polymerase ii subunit rpb2. Chain: b. Synonym: rpb2, RNA polymerase ii subunit 2, b150, DNA-direc polymerase ii 140 kda polypeptide.
Source: Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Saccharomyces cerevisiae, saccharomyce cerevisiae. Yeast, yeast. Organism_taxid: 4932, 4932. Gene: rpb9, ygl070c. Expressed in: escherichia coli.
Resolution:
4.30Å     R-factor:   0.236     R-free:   0.281
Authors: W.Ruan,E.Lehmann,M.Thomm,D.Kostrewa,P.Cramer
Key ref: W.Ruan et al. (2011). Evolution of two modes of intrinsic RNA polymerase transcript cleavage. J Biol Chem, 286, 18701-18707. PubMed id: 21454497 DOI: 10.1074/jbc.M111.222273
Date:
22-Feb-11     Release date:   23-Mar-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04050  (RPB1_YEAST) -  DNA-directed RNA polymerase II subunit RPB1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1733 a.a.
1416 a.a.
Protein chain
Pfam   ArchSchema ?
P08518  (RPB2_YEAST) -  DNA-directed RNA polymerase II subunit RPB2
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1224 a.a.
1103 a.a.
Protein chain
Pfam   ArchSchema ?
P16370  (RPB3_YEAST) -  DNA-directed RNA polymerase II subunit RPB3
Seq:
Struc:
318 a.a.
266 a.a.
Protein chain
Pfam   ArchSchema ?
P20433  (RPB4_YEAST) -  DNA-directed RNA polymerase II subunit RPB4
Seq:
Struc:
221 a.a.
178 a.a.
Protein chain
Pfam   ArchSchema ?
P20434  (RPAB1_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1
Seq:
Struc:
215 a.a.
214 a.a.
Protein chain
Pfam   ArchSchema ?
P20435  (RPAB2_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2
Seq:
Struc:
155 a.a.
87 a.a.
Protein chain
Pfam   ArchSchema ?
P34087  (RPB7_YEAST) -  DNA-directed RNA polymerase II subunit RPB7
Seq:
Struc:
171 a.a.
171 a.a.
Protein chain
Pfam   ArchSchema ?
P20436  (RPAB3_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3
Seq:
Struc:
146 a.a.
134 a.a.
Protein chain
Pfam   ArchSchema ?
P27999  (RPB9_YEAST) -  DNA-directed RNA polymerase II subunit RPB9
Seq:
Struc:
122 a.a.
47 a.a.
Protein chain
Pfam   ArchSchema ?
Q04307  (RPC10_YEAST) -  DNA-directed RNA polymerase III subunit RPC10
Seq:
Struc:
110 a.a.
47 a.a.*
Protein chain
Pfam   ArchSchema ?
P22139  (RPAB5_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5
Seq:
Struc:
70 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P38902  (RPB11_YEAST) -  DNA-directed RNA polymerase II subunit RPB11
Seq:
Struc:
120 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P40422  (RPAB4_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC4
Seq:
Struc:
70 a.a.
46 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 34 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: 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     cytoplasm   8 terms 
  Biological process     transcription, RNA-dependent   20 terms 
  Biochemical function     RNA polymerase II activity     20 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M111.222273 J Biol Chem 286:18701-18707 (2011)
PubMed id: 21454497  
 
 
Evolution of two modes of intrinsic RNA polymerase transcript cleavage.
W.Ruan, E.Lehmann, M.Thomm, D.Kostrewa, P.Cramer.
 
  ABSTRACT  
 
During gene transcription, the RNA polymerase (Pol) active center can catalyze RNA cleavage. This intrinsic cleavage activity is strong for Pol I and Pol III but very weak for Pol II. The reason for this difference is unclear because the active centers of the polymerases are virtually identical. Here we show that Pol II gains strong cleavage activity when the C-terminal zinc ribbon domain (C-ribbon) of subunit Rpb9 is replaced by its counterpart from the Pol III subunit C11. X-ray analysis shows that the C-ribbon has detached from its site on the Pol II surface and is mobile. Mutagenesis indicates that the C-ribbon transiently inserts into the Pol II pore to complement the active center. This mechanism is also used by transcription factor IIS, a factor that can bind Pol II and induce strong RNA cleavage. Together with published data, our results indicate that Pol I and Pol III contain catalytic C-ribbons that complement the active center, whereas Pol II contains a non-catalytic C-ribbon that is immobilized on the enzyme surface. Evolution of the Pol II system may have rendered mRNA transcript cleavage controllable by the dissociable factor transcription factor IIS to enable promoter-proximal gene regulation and elaborate 3'-processing and transcription termination.