Molecular architecture and ligand recognition determinants for T4 RNA ligase.
RNA ligase type 1 from bacteriophage T4 (Rnl1) is involved in countering a host defense mechanism by repairing 5'-PO4 and 3'-OH groups in tRNA(Lys). Rnl1 is widely used as a reagent in molecular biology. Although many structures for DNA ligases are available, only fragments of RNA ligases such as Rnl2 are known. We report the first crystal structure of a complete RNA ligase, Rnl1, in complex with adenosine 5'-(alpha,beta-methylenetriphosphate) (AMPcPP). The N-terminal domain is related to the equivalent region of DNA ligases and Rnl2 and binds AMPcPP but with further interactions from the additional N-terminal 70 amino acids in Rnl1 (via Tyr37 and Arg54) and the C-terminal domain (Gly269 and Asp272). The active site contains two metal ions, consistent with the two-magnesium ion catalytic mechanism. The C-terminal domain represents a new all alpha-helical fold and has a charge distribution and architecture for helix-nucleic acid groove interaction compatible with tRNA binding.
El Omari
Kamel
K
Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
Ren
Jingshan
J
Bird
Louise E
LE
Bona
Marion K
MK
Klarmann
George
G
LeGrice
Stuart F J
SF
Stammers
David K
DK
D017122:Bacteriophage T4 / Q000201:enzymology; D001665:Binding Sites; D003001:Cloning, Molecular; D008024:Ligands; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011130:RNA Ligase (ATP) / Q000737:chemistry* / Q000378:metabolism*; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D014764:Viral Proteins / Q000737:chemistry* / Q000378:metabolism*
D008024:Ligands; D011994:Recombinant Proteins; D014764:Viral Proteins; D011130:RNA Ligase (ATP); C477285:bacteriophage T4 RNA ligase 1; C467724:bacteriophage T4 RNA ligase 2