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PDBsum entry 3h3v

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protein dna_rna metals Protein-protein interface(s) links
Transferase/DNA/RNA PDB id
3h3v
Jmol
Contents
Protein chains
1416 a.a. *
1108 a.a. *
266 a.a. *
177 a.a. *
214 a.a. *
84 a.a. *
171 a.a. *
133 a.a. *
119 a.a. *
65 a.a. *
114 a.a. *
46 a.a. *
DNA/RNA
Metals
_ZN ×8
_MG
* Residue conservation analysis
PDB id:
3h3v
Name: Transferase/DNA/RNA
Title: Yeast rnap ii containing poly(a)-signal sequence in the acti
Structure: DNA-directed RNA polymerase ii subunit rpb1. Chain: b. Synonym: RNA polymerase ii subunit b1, RNA polymerase ii su DNA-directed RNA polymerase iii largest subunit, RNA polyme subunit b220. DNA-directed RNA polymerase ii subunit rpb2. Chain: c. Synonym: RNA polymerase ii subunit 2, DNA-directed RNA poly 140 kda polypeptide, b150.
Source: Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Synthetic: yes. Synthetic: yes
Resolution:
4.00Å     R-factor:   0.205     R-free:   0.241
Authors: S.Dengl,P.Cramer
Key ref: S.Dengl and P.Cramer (2009). Torpedo nuclease Rat1 is insufficient to terminate RNA polymerase II in vitro. J Biol Chem, 284, 21270-21279. PubMed id: 19535338
Date:
17-Apr-09     Release date:   16-Jun-09    
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.
1108 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.
177 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.
84 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.
133 a.a.
Protein chain
Pfam   ArchSchema ?
P27999  (RPB9_YEAST) -  DNA-directed RNA polymerase II subunit RPB9
Seq:
Struc:
122 a.a.
119 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  CATH domain

 Enzyme reactions 
   Enzyme class: Chains B, C: 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   22 terms 
  Biochemical function     RNA polymerase II activity     20 terms  

 

 
    reference    
 
 
J Biol Chem 284:21270-21279 (2009)
PubMed id: 19535338  
 
 
Torpedo nuclease Rat1 is insufficient to terminate RNA polymerase II in vitro.
S.Dengl, P.Cramer.
 
  ABSTRACT  
 
Termination of RNA polymerase (pol) II transcription in vivo requires the 5'-RNA exonuclease Rat1. It was proposed that Rat1 degrades RNA from the 5'-end that is created by transcript cleavage, catches up with elongating pol II, and acts like a Torpedo that removes pol II from DNA. Here we test the Torpedo model in an in vitro system based on bead-coupled pol II elongation complexes (ECs). Recombinant Rat1 complexes with Rai1, and with Rai1 and Rtt103, degrade RNA extending from the EC until they reach the polymerase surface but fail to terminate pol II. Instead, the EC retains an approximately 18-nucleotide RNA that remains with its 3'-end at the active site and can be elongated. Thus, pol II termination apparently requires a factor or several factors in addition to Rat1, Rai1, and Rtt103, post-translational modifications of these factors, or unusual reaction conditions.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21206491 C.Miller, B.Schwalb, K.Maier, D.Schulz, S.Dümcke, B.Zacher, A.Mayer, J.Sydow, L.Marcinowski, L.Dölken, D.E.Martin, A.Tresch, and P.Cramer (2011).
Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast.
  Mol Syst Biol, 7, 458.  
21487437 J.N.Kuehner, E.L.Pearson, and C.Moore (2011).
Unravelling the means to an end: RNA polymerase II transcription termination.
  Nat Rev Mol Cell Biol, 12, 283-294.  
19758983 G.E.Damsma, and P.Cramer (2009).
Molecular basis of transcriptional mutagenesis at 8-oxoguanine.
  J Biol Chem, 284, 31658-31663.
PDB codes: 3i4m 3i4n
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