The capping enzyme is part of the covalent nucleotidyl transferases superfamily, which also includes DNA ligases and RNA ligases.  The enzymes of this superfamily share the following similarities:
* Conserved regions known as motifs I, II, III, IIIa, IV, V and VI, which are arranged in the same order and similar spacing    
* A lysine containing motif KxDG (motif I)
* A covalent lysyl-NMP intermediate
The capping enzyme is composed of two domains, a nucleotidyl transferase (NTase) domain and a C-terminal oligonucleotide binding (OB) domain. The NTase domain, conserved in capping enzymes, DNA and RNA ligases, is made up 5 motifs, I, III, IIIa, IV and V.  Motif I or KxDG is the active site where the covalent (lysyl)-N-GMP intermediate is formed.     Both the NTase and OB domains undergo conformational changes that assist in the capping reaction.
Capping enzymes are found in the nucleus of eukaryotic cells.  Depending on the organism, the capping enzyme is either a monofunctional or bifunctional polypeptide.   The guanylyltransferases (Ceg1) of Saccharomyces cerevisiae is encoded by the CEG1 gene and is composed of 459 amino acids (53-kD). The RNA triphosphatase (Cet1) is a separate 549 amino acid polypeptide (80-kD), encoded by the CET1 gene.  The human capping enzyme is an example of a bifunctional polypeptide, which has both triphosphatase (N-terminal) and guanylyltransferase (C-terminal) domains. The human mRNA guanylyltransferase domain of the capping enzyme is composed of seven helices and fifteen β strands that are grouped into three, five and seven strands, arranged as antiparallel β sheets. The enzyme structure has three sub-domains referred to hinge, base and lid. The GTP binding site is located between the hinge and base domain.  The lid domain determines the conformation of the active site cleft, which consists of the GTP binding site, phosphoamide linking lysine and surrounding residues.  The guanylyltransferase domain is linked to the triphosphatase domain via a 25 amino acid flexible loop structure.