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PDBsum entry 3q23

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protein dna_rna ligands metals Protein-protein interface(s) links
Transferase/DNA PDB id
3q23
Jmol
Contents
Protein chains
1095 a.a. *
DNA/RNA
Ligands
G2P ×4
2HP ×2
Metals
_MN ×4
Waters ×2626
* Residue conservation analysis
PDB id:
3q23
Name: Transferase/DNA
Title: X-ray crystal structure of the n4 mini-vrnap and p2_7a promo transcription initiation complex with gmpcpp and manganese: complex ii
Structure: Virion RNA polymerase. Chain: a, b. Engineered: yes. DNA (5'- d( Tp Gp Cp Cp Tp Cp Cp Cp Ap Gp Gp Cp Ap Tp Cp Cp Ap Ap Ap ap Gp Cp Gp Gp Ap Gp Cp Tp Tp Cp Tp Tp C)-3'). Chain: c, d. Engineered: yes
Source: Enterobacteria phage n4. Bacteriophage n4. Organism_taxid: 10752. Gene: gp50. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes
Resolution:
1.80Å     R-factor:   0.201     R-free:   0.231
Authors: M.L.Gleghorn,K.S.Murakami
Key ref: M.L.Gleghorn et al. (2011). X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides. Proc Natl Acad Sci U S A, 108, 3566-3571. PubMed id: 21321236
Date:
19-Dec-10     Release date:   16-Feb-11    
PROCHECK
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 Headers
 References

Protein chains
Pfam  
Q859P9  (Q859P9_BPN4) -  Virion RNA polymerase
Seq:
Struc:
 
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Seq:
Struc:
3500 a.a.
1095 a.a.
Key:    Secondary structure  CATH domain

 

 
Proc Natl Acad Sci U S A 108:3566-3571 (2011)
PubMed id: 21321236  
 
 
X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.
M.L.Gleghorn, E.K.Davydova, R.Basu, L.B.Rothman-Denes, K.S.Murakami.
 
  ABSTRACT  
 
We have determined the X-ray crystal structures of the pre- and postcatalytic forms of the initiation complex of bacteriophage N4 RNA polymerase that provide the complete set of atomic images depicting the process of transcript initiation by a single-subunit RNA polymerase. As observed during T7 RNA polymerase transcript elongation, substrate loading for the initiation process also drives a conformational change of the O-helix, but only the correct base pairing between the +2 substrate and DNA base is able to complete the O-helix conformational transition. Substrate binding also facilitates catalytic metal binding that leads to alignment of the reactive groups of substrates for the nucleotidyl transfer reaction. Although all nucleic acid polymerases use two divalent metals for catalysis, they differ in the requirements and the timing of binding of each metal. In the case of bacteriophage RNA polymerase, we propose that catalytic metal binding is the last step before the nucleotidyl transfer reaction.