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This Article ACCEPTED PREPRINT Full Text (PDF) Supplemental Research Data All Versions of this Article: ps.034736.108v1 17/11/1915    most recent Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Google Scholar Articles by Kuwahara, Y. Articles by HIROAKI, H. PubMed PubMed Citation Articles by Kuwahara, Y. Articles by HIROAKI, H. Social Bookmarking                   What's this?

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

¹ Yokohama City University;
² Kyoto University;
³ National Institute of Advanced Industrial Science and Technology (AIST);
⁴ Kobe University

(RECEIVED February 4, 2008; ACCEPTED July 2, 2008)

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 β-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 β-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.

Keywords: Protein Structure/Folding; Membrane Proteins; Structure; NMR Spectroscopy; Genomics - Structural; OB-fold

⁵ E-mail: hiroakih{at}med.kobe-u.ac.jp

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