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PDB:1I6H

Protein Name

DNA-DIRECTED RNA POLYMERASE II

Species

Saccharomyces cerevisiae (Baker's yeast)

Biological Context

The genetic code in the DNA is converted to proteins not in a single step, but in two steps called transcription and translation. In the first step DNA is transcribed into messenger RNA (mRNA). This step involves various proteins like transcription initiation factors that start the whole process, and other proteins. One of these other proteins, maybe the most important actor in this play, is the RNA polymerase. RNA polymerase binds DNA, recognizes its sequence and synthesizes RNA. Several functions must be available to such a protein: a place to bind DNA and unwind it and a place to bind RNA and add new nucleotides to the growing RNA chain. Since this protein is so important in the system we call life, knowing its structure is of great interest.

Structure Description

1i6h1i6h_x1i6h_y

Here we see this structure and, even more importantly, see it together with DNA and RNA in the process of doing its job. It is an amazing large structure containing altogether more than 28,000 atoms and made from 10 different types of building blocks. Together they form a very very deep cleft and inside this cleft you can see both DNA and RNA as a hybrid, beautifully illustrating the small, but significant difference between DNA and RNA, the extra oxygen attached to one of the sugar carbons. One can also see how the two coil together to form a double strand with one half being DNA and the other RNA. If we call the side with the deep cleft the front side, then, turning to the back side, where we find the RNA, a tunnel runs through the molecule. Fresh ribonucleotides can enter through this tunnel to reach the site where they will be attached to the growing RNA chain. Considering the size and complexity of this molecule and the fact that it brings so many aspects of molecular biology together in a single structure, one might well want to call it one of the most beautiful structures of the Protein Data Bank for all the features it vividly illustrates.

Protein Data Bank (PDB)

References

Source

Gnatt, A.L. Cramer, P. Fu, J. Bushnell, D.A. Kornberg, R.D.; "Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 angstroms resolution."; Science; (2001) 292:1876-1882 PubMed:11313499.

Others

UniProt:P04050 UniProt:P08518 UniProt:P16370 UniProt:P20434 UniProt:P20435 UniProt:P20436 UniProt:P27999 UniProt:P22139 UniProt:P38902 UniProt:P40422

author: Arno Paehler


Japanese version:PDB:1I6H