1IPA

CRYSTAL STRUCTURE OF RNA 2'-O RIBOSE METHYLTRANSFERASE

Summary for 1IPA

• Entry DOI: 10.2210/pdb1ipa/pdb
• Descriptor: RNA 2'-O-RIBOSE METHYLTRANSFERASE (2 entities in total)
• Functional Keywords: deep trefoil knot, rossmann fold, el30-like fold, riken structural genomics/proteomics initiative, rsgi, structural genomics, transferase
• Biological source: Thermus thermophilus
• Total number of polymer chains: 1
• Total formula weight: 30017.45

Authors

Nureki, O.,Shirouzu, M.,Hashimoto, K.,Ishitani, R.,Terada, T.,Tamakoshi, M.,Oshima, T.,Chijimatsu, M.,Takio, K.,Vassylyev, D.G.,Shibata, T.,Inoue, Y.,Kuramitsu, S.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2001-05-02, release date: 2002-07-10, Last modification date: 2023-12-27)

Primary citation

Nureki, O.,Shirouzu, M.,Hashimoto, K.,Ishitani, R.,Terada, T.,Tamakoshi, M.,Oshima, T.,Chijimatsu, M.,Takio, K.,Vassylyev, D.G.,Shibata, T.,Inoue, Y.,Kuramitsu, S.,Yokoyama, S.
An enzyme with a deep trefoil knot for the active-site architecture.
Acta Crystallogr.,Sect.D, 58:1129-1137, 2002

PubMed Abstract: Knots in polypeptide chains have been found in very few proteins. Only two proteins are considered to have a shallow 'trefoil' knot, which tucks a few residues at one end of the chain through a loop exposed on the protein surface. Recently, another protein was found by a mathematical algorithm to have a deep 'figure-of-eight' knot which had not been visually identified. In the present study, the crystal structure of a hypothetical RNA 2'-O-ribose methyltransferase from Thermus thermophilus (RrmA) was determined at 2.4 A resolution and a deep trefoil knot was found for the first time. The present knot is formed by the threading of a 44-residue polypeptide chain through a 41-residue loop and is better defined than the previously reported knots. Two of the three catalytic residues conserved in the 2'-O-ribose methyltransferase family are located in the knotting loop and in the knotted carboxy-terminal chain, which is the first observation that the enzyme active site is constructed right on the knot. On the other hand, the amino-terminal domain exhibits a geometrical similarity to the ribosomal proteins which recognize an internal loop of RNA.

PubMed: 12077432
DOI: 10.1107/S0907444902006601

Experimental method

X-RAY DIFFRACTION (2.4 Å)