PDBsum entry 1nyn

Structural genomics, unknown function

PDB id: 1nyn

Contents

Protein chain

111 a.a. *

* Residue conservation analysis

PDB id:

1nyn

Name:

Structural genomics, unknown function

Title:

Solution nmr structure of protein yhr087w from saccharomyces cerevisiae. Northeast structural genomics consortium target ytyst425.

Structure:

Hypothetical 12.0 kda protein in nam8-gar1 intergenic region. Chain: a. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: yhr087w. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

20 models

Authors:

J.R.Cort,A.A.Yee,C.H.Arrowsmith,M.A.Kennedy,Northeast Structural Genomics Consortium (Nesg)

Key ref:

A.Savchenko et al. (2005). The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism. J Biol Chem, 280, 19213-19220. PubMed id: 15701634 DOI: 10.1074/jbc.M414421200

Date:

13-Feb-03 Release date: 08-Apr-03

Protein chain

P38804  (SDO1L_YEAST) -  Restriction of telomere capping protein 3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 111 a.a.

Struc: 111 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1074/jbc.M414421200

J Biol Chem 280:19213-19220 (2005)

PubMed id: 15701634

The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism.

A.Savchenko, N.Krogan, J.R.Cort, E.Evdokimova, J.M.Lew, A.A.Yee, L.Sánchez-Pulido, M.A.Andrade, A.Bochkarev, J.D.Watson, M.A.Kennedy, J.Greenblatt, T.Hughes, C.H.Arrowsmith, J.M.Rommens, A.M.Edwards.

ABSTRACT

A combination of structural, biochemical, and genetic studies in model organisms was used to infer a cellular role for the human protein (SBDS) responsible for Shwachman-Bodian-Diamond syndrome. The crystal structure of the SBDS homologue in Archaeoglobus fulgidus, AF0491, revealed a three domain protein. The N-terminal domain, which harbors the majority of disease-linked mutations, has a novel three-dimensional fold. The central domain has the common winged helix-turn-helix motif, and the C-terminal domain shares structural homology with known RNA-binding domains. Proteomic analysis of the SBDS sequence homologue in Saccharomyces cerevisiae, YLR022C, revealed an association with over 20 proteins involved in ribosome biosynthesis. NMR structural genomics revealed another yeast protein, YHR087W, to be a structural homologue of the AF0491 N-terminal domain. Sequence analysis confirmed them as distant sequence homologues, therefore related by divergent evolution. Synthetic genetic array analysis of YHR087W revealed genetic interactions with proteins involved in RNA and rRNA processing including Mdm20/Nat3, Nsr1, and Npl3. Our observations, taken together with previous reports, support the conclusion that SBDS and its homologues play a role in RNA metabolism.

Selected figure(s)

Figure 2.
FIG. 2. Structural comparison of YHR087W and AF0491. A, stereo image of 20 superimposed NMR structures of S. cerevisiae YHR087W. B, secondary structure of the AF0491 N-terminal domain.

Figure 4.
FIG. 4. Electrostatic surface potential for YHR087W and AF0491 N-terminal domain. A, electrostatic surface potential for YHR087W. B, electrostatic surface potential for AF0491 N-terminal domain. Red and blue indicate potentials <-8 and >+8 k[B]T respectively, where k[B] is the Boltzmann constant and T is temperature (K). Aligned ribbon structures for YHR087W and AF0491 N-terminal domain are shown next to the corresponding electrostatic surfaces for the same and opposite sides of each structure as indicated. Calculations were made with GRASP (68).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 19213-19220) copyright 2005.

Figures were selected by an automated process.