Crystal of bacterial core RNA polymerase and methods of use thereof

Abstract

A detailed three-dimensional structure for a bacterial core RNA polymerase is provided. Crystals of the bacterial core RNA polymerase are also included in the invention. The present invention further provides procedures for identifying agents that can inhibit bacterial proliferation through the use of rational drug design predicated on the crystals and crystallographic data disclosed.

1 - 22 . (canceled)  
     
     
         23 . A crystallized polypeptide comprising: (a) at least one of the amino acid sequences set forth in SEQ ID NO: 1 or SEQ ID NO: 2 or SEQ ID NO: 3; or (b) an amino acid sequence that is substantially similar to at least one of the amino acid sequences set forth in SEQ ID NO: 1 or SEQ ID NO: 2 or SEQ ID NO: 3; and has at least one biological activity of a core RNA polymerase from  Thermus aquaticus  wherein the polypeptide of (a), (b) or (c) is in crystal form and wherein said crystallized polypeptide diffracts x-rays to a resolution of about 3.5 Å or better for the determination of the three-dimensional atomic coordinates of said core RNA polymerase.  
     
     
         24 . The crystallized polypeptide of  claim 23 , wherein said crystallized polypeptide comprises an amino acid sequence that has at least about 80% sequence homology to at least one of the amino acid sequences set forth in SEQ ID NO: 1 or SEQ ID NO: 2 or SEQ ID NO: 3.  
     
     
         25 . The crystallized polypeptide of  claim 23 , wherein said crystallized polypeptide comprises an amino acid sequence that has at least about 85% sequence homology to at least one of the amino acid sequences set forth in SEQ ID NO: 1 or SEQ ID NO: 2or SEQ ID NO: 3.  
     
     
         26 . The crystallized polypeptide of  claim 23 , wherein said crystallized polypeptide comprises an amino acid sequence that has at least about 90% sequence homology to at least one of the amino acid sequences set forth in SEQ ID NO: 1 or SEQ ID NO: 2 or SEQ ID NO: 3.  
     
     
         27 . The crystallized polypeptide of  claim 23 , wherein said crystallized polypeptide comprises an amino acid sequence that has at least about 95% sequence homology to at least one of the amino acid sequences set forth in SEQ ID NO: 1 or SEQ ID NO: 2or SEQ ID NO: 3.  
     
     
         28 . The crystallized polypeptide of  claim 23 , wherein the crystal has a P41212 space group.  
     
     
         29 . The crystallized polypeptide of  claim 23 , which diffracts x-rays to a resolution of about 3.3 Å or better.  
     
     
         30 . The crystallized polypeptide of  claim 23 , wherein the polypeptide is derivatized with at least one heavy metal atom.  
     
     
         31 . The crystallized polypeptide of  claim 30 , wherein the polypeptide is derivatized with selenium.  
     
     
         32 . The crystallized polypeptide of  claim 30 , wherein the polypeptide is derivatized with one of the following: mercury, lead, or tantalum.  
     
     
         33 . The crystallized polypeptide of  claim 23 , further comprising a cryoprotectant.  
     
     
         34 . The crystallized polypeptide of  claim 28 , wherein said cryoprotectant is sucrose.