PDBsum entry 1r8c

Transferase

PDB id: 1r8c

Contents

Protein chain

437 a.a. *

Ligands

UTP ×2

Metals

_MN ×5

_NA

Waters ×328

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structures of an archaeal class I cca-Adding enzyme and its nucleotide complexes.

Authors

Y.Xiong, F.Li, J.Wang, A.M.Weiner, T.A.Steitz.

Ref.

Mol Cell, 2003, 12, 1165-1172. [DOI no: 10.1016/S1097-2765(03)00440-4]

PubMed id

14636575

Abstract

CCA-adding enzymes catalyze the addition of CCA onto the 3' terminus of immature tRNAs without using a nucleic acid template and have been divided into two classes based on their amino acid sequences. We have determined the crystal structures of a class I CCA-adding enzyme from Archeoglobus fulgidus (AfCCA) and its complexes with ATP, CTP, or UTP. Although it and the class II bacterial Bacillus stearothermophilus CCA enzyme (BstCCA) have similar dimensions and domain architectures (head, neck, body, and tail), only the polymerase domain is structurally homologous. Moreover, the relative orientation of the head domain with respect to the body and tail domains, which appear likely to bind tRNA, differs significantly between the two enzyme classes. Unlike the class II BstCCA, this enzyme binds nucleotides nonspecifically in the absence of bound tRNA. The shape and electrostatic charge distribution of the AfCCA enzyme suggests a model for tRNA binding that accounts for the phosphates that are protected from chemical modification by tRNA binding to AfCCA. The structures of the AfCCA enzyme and the eukaryotic poly(A) polymerase are very similar, implying a close evolutionary relationship between them.

Figure 2.
Figure 2. A Comparison of the Structures of the Polymerase Domains of AfCCA, BstCCA, and DNA pol βThe polymerase domain is shown in magenta and the neck/fingers in green. The incoming nucleotide is yellow and the metal ions are brown. The three catalytic carboxylates are shown. In (B), the last magenta helix (cylinder) to the right belongs to pol β fingers domain. For comparison with the AfCCA head it is colored the same as the palm domain. In (C), the region colored in red represents the additional part of BstCCA not seen in the AfCCA head and Pol β domains.

Figure 5.
Figure 5. A Comparison of the Different Orientations that the tRNA Acceptor Stem and TΨC Stem-Loop Have with Respect to the Head Domains in the Two Classes of CCA-Adding Enzyme(A) AfCCA. (B) BstCCA. The head domains of the two enzymes are represented in magenta ribbons and are in the same orientation. The enzymes are shown with surface representation and the acceptor stem and TψC stem-loop of the tRNA in yellow coil.

The above figures are reprinted by permission from Cell Press: Mol Cell (2003, 12, 1165-1172) copyright 2003.