PDBsum entry: 1oxj

RNA binding protein

PDB id: 1oxj

Contents

Protein chain

170 a.a. *

Waters ×163

* Residue conservation analysis

PDB id:

1oxj

Name:

RNA binding protein

Title:

Crystal structure of the smaug RNA binding domain

Structure:

RNA-binding protein smaug. Chain: a. Fragment: RNA binding domain, sam domain. Engineered: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: smg. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Trimer (from PQS)

Resolution:

1.80Å R-factor: 0.229 R-free: 0.244

Authors:

J.B.Green,C.D.Gardner,R.P.Wharton,A.K.Aggarwal

Key ref:

J.B.Green et al. (2003). RNA recognition via the SAM domain of Smaug. Mol Cell, 11, 1537-1548. PubMed id: 12820967 DOI: 10.1016/S1097-2765(03)00178-3

Date:

02-Apr-03 Release date: 08-Jul-03

Protein chain

Q23972  (SMG_DROME) -  Protein Smaug

Seq: 999 a.a.

Struc: 170 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Biochemical function: binding (1 term)

DOI no: 10.1016/S1097-2765(03)00178-3

Mol Cell 11:1537-1548 (2003)

PubMed id: 12820967

RNA recognition via the SAM domain of Smaug.

J.B.Green, C.D.Gardner, R.P.Wharton, A.K.Aggarwal.

ABSTRACT

The Nanos protein gradient in Drosophila, required for proper abdominal segmentation, is generated in part via translational repression of its mRNA by Smaug. We report here the crystal structure of the Smaug RNA binding domain, which shows no sequence homology to any previously characterized RNA binding motif. The structure reveals an unusual makeup in which a SAM domain, a common protein-protein interaction module, is affixed to a pseudo-HEAT repeat analogous topology (PHAT) domain. Unexpectedly, we find through a combination of structural and genetic analysis that it is primarily the SAM domain that interacts specifically with the appropriate nanos mRNA regulatory sequence. Therefore, in addition to their previously characterized roles in protein-protein interactions, some SAM domains play crucial roles in RNA binding.

Selected figure(s)

Figure 4.
Figure 4. Smg PHAT DomainSmg PHAT domain (orange) is shown aligned above two and a half HEAT repeats of protein phosphatase 2a (pp2a) (purple). The Smg PHAT domain aligns with this segment of pp2A with an rmsd of vert, similar 2.4 Å (at 83 Cα pairs). The topology of each protein segment is shown schematically alongside the ribbon diagrams.

Figure 5.
Figure 5. Smg Recognizes RNA via Its SAM DomainOn the right, the electrostatic potential is mapped on the Smg RBD surface with increasing blue signifying increasing electropositivity and increasing red indicating increasing electronegativity. On the left, the 51 silent substitutions that do not significantly affect RNA binding are mapped on the surface in green; residues where no silent substitutions were recovered are white. The top view is related to the orientation in Figure 2A by a rotation of 90° about the vertical axis of the page. Note that the electropositive surface of the SAM domain is devoid of silent substitutions, consistent with the idea that it makes the majority of the RNA contacts.

The above figures are reprinted by permission from Cell Press: Mol Cell (2003, 11, 1537-1548) copyright 2003.

Figures were selected by an automated process.