PDBsum entry 2exd

Membrane protein

PDB id: 2exd

Contents

Protein chain

74 a.a. *

* Residue conservation analysis

PDB id:

2exd

Name:

Membrane protein

Title:

The solution structure of thE C-terminal domain of a nfed homolog from pyrococcus horikoshii

Structure:

Nfed short homolog. Chain: a. Fragment: residues 72-143. Engineered: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. Gene: ph0471. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

Y.Kuwahara,A.Ohno,T.Morii,H.Tochio,M.Shirakawa,H.Hiroaki

Key ref:

Y.Kuwahara et al. (2008). The solution structure of the C-terminal domain of NfeD reveals a novel membrane-anchored OB-fold. Protein Sci, 17, 1915-1924. PubMed id: 18687870 DOI: 10.1110/ps.034736.108

Date:

08-Nov-05 Release date: 12-Dec-06

Protein chain

O58204  (O58204_PYRHO) -  NfeD-like C-terminal domain-containing protein from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: 143 a.a.

Struc: 74 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1110/ps.034736.108

Protein Sci 17:1915-1924 (2008)

PubMed id: 18687870

The solution structure of the C-terminal domain of NfeD reveals a novel membrane-anchored OB-fold.

Y.Kuwahara, A.Ohno, T.Morii, H.Yokoyama, I.Matsui, H.Tochio, M.Shirakawa, H.Hiroaki.

ABSTRACT

Nodulation formation efficiency D (NfeD) is a member of a class of membrane-anchored ClpP-class proteases. There is a second class of NfeD homologs that lack the ClpP domain. The genes of both NfeD classes usually are part of an operon that also contains a gene for a prokaryotic homolog of stomatin. (Stomatin is a major integral-membrane protein of mammalian erythrocytes.) Such NfeD/stomatin homolog gene pairs are present in more than 290 bacterial and archaeal genomes, and their protein products may be part of the machinery used for quality control of membrane proteins. Herein, we report the structure of the isolated C-terminal domain of PH0471, a Pyrococcus horikoshii NfeD homolog, which lacks the ClpP domain. This C-terminal domain (termed NfeDC) contains a five-strand beta-barrel, which is structurally very similar to the OB-fold (oligosaccharide/oligonucleotide-binding fold) domain. However, there is little sequence similarity between it and previously characterized OB-fold domains. The NfeDC domain lacks the conserved surface residues that are necessary for the binding of an OB-fold domain to DNA/RNA, an ion. Instead, its surface is composed of residues that are uniquely conserved in NfeD homologs and that form the structurally conserved surface turns and beta-bulges. There is also a conserved tryptophan present on the surface. We propose that, in general, NfeDC domains may interact with other spatially proximal membrane proteins and thereby regulate their activities.

Selected figure(s)

Figure 2.
Solution structure of PH0471^NfeDC. (A) A stereoview of the best fit superposition of the 20 structures with the least number of structural violations. (B, front, above and top, below) Stereoviews of a ribbon diagram showing the overall fold of PH0471^NfeDC. The navy, sky blue, cyan, yellow, and green strands correspond to strands [beta]1 --[beta]5. (C) A topology diagram. Experimentally identified hydrogen bonds are indicated by red dashed lines. Bulged residues are accentuated by bold circles. (D) The five-residue turn of residues 105 --109. (E) The hydrophobic core of PH0471^NfeDC. Conserved hydrophobic residues are colored red. The side chain of W111 is colored navy blue.

Figure 4.
Ribbon diagrams of OB-folds found for six proteins other than PH0471^NfeDC that were retrieved from a DALI-server search (Holm and Sander 1997). (A) The N-terminal domain of the ribosomal-binding GTPase, YjeQ (PDB 1u0l). (B) The E. coli major cold-shock protein, CspA (1mjc). (C) The ribosomal protein, S17 (2f4v-chain Q). (D) Toxic shock syndrome toxin-1 TSST-1 (1aw7). (E) The molybdate-binding protein (1h9j). (F) The E. coli periplasmic cupper resistance protein, CusF (1zeq). The navy, sky blue, cyan, yellow, and green strands correspond to strands [beta]1 --[beta]5 of PH0471^NfeDC, respectively. For each protein, the side chains that participate in ligand binding, as discussed in text, are colored red.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2008, 17, 1915-1924) copyright 2008.

Figures were selected by an automated process.