5EAQ

Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mn2+

Summary for 5EAQ

• Entry DOI: 10.2210/pdb5eaq/pdb
• Related: 5EAO
• Descriptor: RNA (48-MER), RNA (5'-R(*GP*GP*GP*CP*GP*U*(CVC)*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3'), MANGANESE (II) ION (3 entities in total)
• Functional Keywords: ribozyme, hammerhead, rna
• Biological source: synthetic construct; More
• Total number of polymer chains: 2
• Total formula weight: 22366.75

Authors

Mir, A.,Golden, B.L. (deposition date: 2015-10-16, release date: 2016-02-24, Last modification date: 2023-09-27)

Primary citation

Mir, A.,Golden, B.L.
Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.
Biochemistry, 55:633-636, 2016

PubMed Abstract: The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.

PubMed: 26551631
DOI: 10.1021/acs.biochem.5b01139

Experimental method

X-RAY DIFFRACTION (3.201 Å)