PDBsum entry 3q22

Transferase/DNA

PDB id: 3q22

Contents

Protein chains

1095 a.a. *

DNA/RNA

Ligands

GTP ×4

2HP ×2

Metals

_MG ×2

Waters ×1420

* Residue conservation analysis

PDB id:

3q22

Name:

Transferase/DNA

Title:

X-ray crystal structure of the n4 mini-vrnap and p2_7a promoter transcription initiation complex with gtp and magnesium: substrate complex i

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 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:

2.11Å R-factor: 0.209 R-free: 0.219

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

Protein chains

Q859P9  (RPOLV_BPN4) -  Virion DNA-directed RNA polymerase from Enterobacteria phage N4

Seq: 3500 a.a.

Struc: 1095 a.a.

DNA/RNA chains

C-C-A-A-A-A-G-A-A-G-C-G-G-A-G-C-T-T-C-T 20 bases

T-C-C-A-A-A-A-G-A-A-G-C-G-G-A-G-C-T-T-C-T 21 bases

Enzyme reactions

• Enzyme class: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

RNA(n) + ribonucleoside 5'-triphosphate = RNA(n+1) (Bound ligand (Het Group name = 2HP) matches with 55.56% similarity) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

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.