DNA-directed RNA polymerase
Ligand-induced domain movement details

Jmol view of liganded conformation 2

Domain Movement

domain 1 is binding domain(fixed in space) domain 2 is binding domain(fixed in space)

Sequence


           __________________________________________________ 
 1h38(A) : NTINIAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARF 
         :                                                    
 1s77(D) : **********SDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARF 
           __________________________________________________ 

           __________________________________________________ 
 1h38(A) : RKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPT 
         :                                                    
 1s77(D) : RKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPT 
           __________________________________________________ 

           __________________________________________________ 
 1h38(A) : AFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARF 
         :                                                    
 1s77(D) : AFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARF 
           __________________________________________________ 

           __________________________________________________ 
 1h38(A) : GRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAW 
         :                                                    
 1s77(D) : GRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKG-----AW 
           __________________________________________________ 

           __________________________________________________ 
 1h38(A) : SSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEYA 
         :                                                    
 1s77(D) : SSWHKEDSIHVGVRCIEMLIESTGMVSLH----------sETIELAPEYA 
           __________________________________________________ 

           __________________________________________________ 
 1h38(A) : EAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHS 
         :                                                    
 1s77(D) : EAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHS 
           __________________________________________________ 

           __________________________________________________ 
 1h38(A) : KKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVED 
         :                                                    
 1s77(D) : KKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVED 
           __________________________________________________ 

           __________________________________________________ 
 1h38(A) : IPAIe-ALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWF 
         :                                                    
 1s77(D) : IPAIEREELPwKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWF 
           __________________________________________________ 

           __________________________________________________ 
 1h38(A) : PYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGAN 
         :                                                    
 1s77(D) : PYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGAN 
           __________________________________________________ 

           __________________________________________________ 
 1h38(A) : CAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCF 
         :                                                    
 1s77(D) : CAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCF 
           __________________________________________________ 

           __________________________________________________ 
 1h38(A) : EYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSET 
         :                                                    
 1s77(D) : EYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSET 
           __________________________________________________ 

           569_______________________________________________ 
 1h38(A) : VQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKAL 
         :                                                    
 1s77(D) : VQDIYGIVAKKVNEILQADAINGTDNEVV--------------KLGTKAL 
           569_______________________________________________ 

           __________________________________________________ 
 1h38(A) : AGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLM 
         :                                                    
 1s77(D) : AGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLM 
           __________________________________________________ 

           ____________681___________________________________ 
 1h38(A) : FTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTG 
         :                                                    
 1s77(D) : FTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTG 
           ____________681___________________________________ 

           __________________________________________________ 
 1h38(A) : EILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFR---------d 
         :                                                    
 1s77(D) : EILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKD 
           __________________________________________________ 

           __________________________________________________ 
 1h38(A) : SEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGT 
         :                                                    
 1s77(D) : SEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGT 
           __________________________________________________ 

           __________________________________________________ 
 1h38(A) : IPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPA 
         :                                                    
 1s77(D) : IPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPA 
           __________________________________________________ 

           _________________                                  
 1h38(A) : KGNLNLRDILESDFAFA                                  
         :                                                    
 1s77(D) : KGNLNLRDILESDFAFA                                  
           _________________                                  

Details

  Property   Value
 Conformer 1 1h38(A)
 Conformer 2 1s77(D)
 Radius gyration for conformer 1 31.28 A
 Radius gyration for conformer 2 30.71 A
 EC Number 2.7.7.6  
Click here to see the DynDom results or the famliy
 Trigger ligands POP901
 Trigger ligands in which conformation Conformation  2
 Conformaton with trigger ligands is compact Yes
 Spanning ligands Yes
 Residues in enzyme contacting ligands ARG627  ASP537  CYS540  GLY538  LYS472  LYS631  SER539  TYR571 
 Residues in extended bending regions contacting ligands TYR571 
 Residues in extended bending regions making H-bonds or salt-bridges with ligands TYR571 
  Residues in extended bending regions with an H-bond between its main chain and ligands Null
Click here to see the details of H-bonds between ligands and enzyme in PDF format generated by LIGPLOT