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2dra A:258-437 PDB entry domain

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   PAP/Archaeal CCA-adding enzyme, C-terminal domain [ 55003] (2)
Family:   Archaeal tRNA CCA-adding enzyme [ 102995]
Protein:   tRNA nucleotidyltransferase, C-terminal domain [102996]
   
PDB Entry Domain:   2dra A:258-437 [ 131668]
  SUPERFAMILY domain annotation for 2draa258-437
  PDB structure summary for 2dra


InterPro annotation
Cross references IPR011068 SSF55003 Protein matches
Abstract

Nucleotidytransferases can be divided into two classes based on highly conserved features of the nucleotidyltransferase motif [PubMed8809016]. Class I enzymes include eukaryotic poly(A) polymerase (PAP), archaeal tRNA CCA-adding enzyme and possibly DNA polymerase beta, while class II enzymes include eukaryotic and eubacterial tRNA CCA-adding enzymes. This entry represents the C-terminal domain of class I nucleotidyltransferases. The C-terminal domain has an alpha/beta sandwich fold, although the archaeal tRNA CCA-adding enzyme has a large insertion; this fold is reminiscent of the RNA-recognition motif fold.

Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase that specifically incorporates ATP at the 3' end of mRNA. In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. The catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase [PubMed10944102]. The three invariant aspartates of the catalytic triad ligate two of the three active site metals. One of these metals also contacts the adenine ring. Furthermore, conserved, catalytically important residues contact the nucleotide. These contacts, taken together with metal coordination of the adenine base, provide a structural basis for ATP selection by poly(A) polymerase.

The archaeal CCA-adding enzyme builds and repairs the 3 ' end of tRNA. A single active site (nucleotidyltransferase motif) adds both CTP and ATP [PubMed15590678]. This enzyme is the only RNA polymerase that can build or rebuild a specific nucleic acid sequence without using a nucleic acid template.


InterPro database

PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

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Internal database links

   
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