PDBsum entry 1jbm

Structural genomics

PDB id: 1jbm

Contents

Protein chains

78 a.a. *

73 a.a. *

Ligands

ACY ×5

EDO ×11

Waters ×273

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The oligomerization and ligand-Binding properties of sm-Like archaeal proteins (smaps).

Authors

C.Mura, A.Kozhukhovsky, M.Gingery, M.Phillips, D.Eisenberg.

Ref.

Protein Sci, 2003, 12, 832-847. [DOI no: 10.1110/ps.0224703]

PubMed id

12649441

Abstract

Intron splicing is a prime example of the many types of RNA processing catalyzed by small nuclear ribonucleoprotein (snRNP) complexes. Sm proteins form the cores of most snRNPs, and thus to learn principles of snRNP assembly we characterized the oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs) from Pyrobaculum aerophilum (Pae) and Methanobacterium thermautotrophicum (Mth). Ultracentrifugation shows that Mth SmAP1 is exclusively heptameric in solution, whereas Pae SmAP1 forms either disulfide-bonded 14-mers or sub-heptameric states (depending on the redox potential). By electron microscopy, we show that Pae and Mth SmAP1 polymerize into bundles of well ordered fibers that probably form by head-to-tail stacking of heptamers. The crystallographic results reported here corroborate these findings by showing heptamers and 14-mers of both Mth and Pae SmAP1 in four new crystal forms. The 1.9 A-resolution structure of Mth SmAP1 bound to uridine-5'-monophosphate (UMP) reveals conserved ligand-binding sites. The likely RNA binding site in Mth agrees with that determined for Archaeoglobus fulgidus (Afu) SmAP1. Finally, we found that both Pae and Mth SmAP1 gel-shift negatively supercoiled DNA. These results distinguish SmAPs from eukaryotic Sm proteins and suggest that SmAPs have a generic single-stranded nucleic acid-binding activity.

Figure 4.
Figure 4. Various crystalline oligomers of Pae and Mth SmAP1. A unit cell of the Pae SmAP1 C222[1] crystal form is shown in (A), along with examples of crystallographic twofold and 2[1] screw axes. The asymmetric unit is a heptamer (shown as C traces in red or blue), and a Pae SmAP1 14-mer with 72-point group symmetry is formed from adjacent asymmetric units (7550 Å2 of surface area is buried at the heptamer-heptamer interface). Orthogonal views of the quasihexagonal packing of Mth SmAP1 heptamers in the P2[1]2[1]2[1] crystal form are shown in (B). Heptamers stack upon one another to form cylindrical tubes, thus providing a model for the structure of the EM fibrils (see text for explanation). The head-to-tail association of heptamers gives the tubes a defined polarity (colored arrows). Molecular surfaces show that the lateral packing of tubes in the crystal may generate the striated bundles seen by EM.

Figure 5.
Figure 5. Ligand-binding sites in the structures of Mth and Pae 14-mers bound to UMP. The two Mth heptamers (red, blue) in the asymmetric unit of the P2[1] form are shown in (A). A single molecule of MPD binds identically to each monomer (space-filling, colored by atom type with yellow carbons). Space-filling models of the 14 UMP ligands show that they bind in the pore region (colored by atom type, gray carbons). Electron density for a UMP binding site is shown in (B). The 2|F[o]| - |F[c]| density is contoured at +1.2 (green) and |F[o]| - |F[c]| maps are contoured at -3.2 (red) or +3.2 (blue). Conserved residues that form the UMP binding sites are labeled, and residues from different monomers are distinguished by primes. Hydrogen-bond distances are not shown, for the sake of clarity (see Fig. 6 Go-). Orthogonal views are shown in (C) for the Pae SmAP1 14-mer in the C222[1] lattice (heptamer per a.u.). Ten glycerol molecules bind to each heptamer (space-filling, green-colored carbons), and seven of them occupy identical sites. Only the uridine fragments of UMP were modeled (space-filling, gray-colored carbons), at identical sites distal to the pore region.

The above figures are reprinted by permission from the Protein Society: Protein Sci (2003, 12, 832-847) copyright 2003.