title: Alternative conformations of the archaeal Nop56/58-fibrillarin complex imply flexibility in box C/D RNPs.
abstract: The Nop56/58-fibrillarin heterocomplex is a core protein complex of the box C/D ribonucleoprotein particles that modify and process ribosomal RNAs. The previous crystal structure of the Archaeoglobus fulgidus complex revealed a symmetric dimer of two Nop56/58-fibrillarin complexes linked by the coiled-coil domains of the Nop56/68 proteins. However, because the A. fulgidus Nop56/58 protein lacks some domains found in most other species, it was thought that the bipartite architecture of the heterocomplex was not likely a general phenomenon. Here we report the crystal structure of the Nop56/58-fibrillarin complex bound with methylation cofactor, S-adenosyl-L-methionine from Pyrococcus furiosus, at 2.7 A. The new complex confirms the generality of the previously observed bipartite arrangement. In addition however, the conformation of Nop56/58 in the new structure differs substantially from that in the earlier structure. The distinct conformations of Nop56/58 suggest potential flexibility in Nop56/58. Computational normal mode analysis supports this view. Importantly, fibrillarin is repositioned within the two complexes. We propose that hinge motion within Nop56/58 has important implications for the possibility of simultaneously positioning two catalytic sites at the two target sites of a bipartite box C/D guide RNA.
authors.affiliation: Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
authors.forename: Sri
authors.initials: S
authors.lastname: Oruganti
authors.forename: Yanming
authors.initials: Y
authors.lastname: Zhang
authors.forename: Hongzhi
authors.initials: H
authors.lastname: Li
authors.forename: Howard
authors.initials: H
authors.lastname: Robinson
authors.forename: Michael P
authors.initials: MP
authors.lastname: Terns
authors.forename: Rebecca M
authors.initials: RM
authors.lastname: Terns
authors.forename: Wei
authors.initials: W
authors.lastname: Yang
authors.forename: Hong
authors.initials: H
authors.lastname: Li
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry*; D019611:Archaeoglobus fulgidus / Q000378:metabolism*; D020134:Catalytic Domain; D002868:Chromosomal Proteins, Non-Histone / Q000737:chemistry*; D018360:Crystallography, X-Ray; D008745:Methylation; D009687:Nuclear Proteins / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D020027:Pyrococcus furiosus / Q000378:metabolism*; D012313:RNA / Q000737:chemistry; D012261:Ribonucleoproteins / Q000737:chemistry*; D012436:S-Adenosylmethionine / Q000737:chemistry
chemical_list: D019843:Archaeal Proteins; D002868:Chromosomal Proteins, Non-Histone; D009687:Nuclear Proteins; D012261:Ribonucleoproteins; C047458:fibrillarin; D012313:RNA; D012436:S-Adenosylmethionine