Dataset Information

Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution.

ABSTRACT: ECX21941 represents a very large family (over 600 members) of novel, ocean metagenome-specific proteins identified by clustering of the dataset from the Global Ocean Sampling expedition. The crystal structure of ECX21941 reveals unexpected similarity to Sm/LSm proteins, which are important RNA-binding proteins, despite no detectable sequence similarity. The ECX21941 protein assembles as a homopentamer in solution and in the crystal structure when expressed in Escherichia coli and represents the first pentameric structure for this Sm/LSm family of proteins, although the actual oligomeric form in vivo is currently not known. The genomic neighborhood analysis of ECX21941 and its homologs combined with sequence similarity searches suggest a cyanophage origin for this protein. The specific functions of members of this family are unknown, but our structure analysis of ECX21941 indicates nucleic acid-binding capabilities and suggests a role in RNA and/or DNA processing.

SUBMITTER: Das D

PROVIDER: S-EPMC2785455 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution.

Das Debanu D Kozbial Piotr P Axelrod Herbert L HL Miller Mitchell D MD McMullan Daniel D Krishna S Sri SS Abdubek Polat P Acosta Claire C Astakhova Tamara T Burra Prasad P Carlton Dennis D Chen Connie C Chiu Hsiu-Ju HJ Clayton Thomas T Deller Marc C MC Duan Lian L Elias Ylva Y Elsliger Marc-André MA Ernst Dustin D Farr Carol C Feuerhelm Julie J Grzechnik Anna A Grzechnik Slawomir K SK Hale Joanna J Han Gye Won GW Jaroszewski Lukasz L Jin Kevin K KK Johnson Hope A HA Klock Heath E HE Knuth Mark W MW Kumar Abhinav A Marciano David D Morse Andrew T AT Murphy Kevin D KD Nigoghossian Edward E Nopakun Amanda A Okach Linda L Oommachen Silvya S Paulsen Jessica J Puckett Christina C Reyes Ron R Rife Christopher L CL Sefcovic Natasha N Sudek Sebastian S Tien Henry H Trame Christine C Trout Christina V CV van den Bedem Henry H Weekes Dana D White Aprilfawn A Xu Qingping Q Hodgson Keith O KO Wooley John J Deacon Ashley M AM Godzik Adam A Lesley Scott A SA Wilson Ian A IA

Proteins 20090501 2

ECX21941 represents a very large family (over 600 members) of novel, ocean metagenome-specific proteins identified by clustering of the dataset from the Global Ocean Sampling expedition. The crystal structure of ECX21941 reveals unexpected similarity to Sm/LSm proteins, which are important RNA-binding proteins, despite no detectable sequence similarity. The ECX21941 protein assembles as a homopentamer in solution and in the crystal structure when expressed in Escherichia coli and represents the ...[more]

PMID: 19173316

Similar Datasets

Project description:Hepatitis E virus (HEV) is a 7.2-kb positive-sense, single-stranded RNA virus containing three partially overlapping reading frames, ORF1 to ORF3. All nonstructural proteins required for viral replication are encoded by ORF1 and are transcribed as a single transcript. Computational analysis of the complete ORF1 polyprotein identified a previously uncharacterized region of predicted secondary structure bordered by two disordered regions coinciding partially with a region predicted as a putative cysteine protease. Following successful cloning, expression, and purification of this region, the crystal structure of the identified protein was determined and identified to have considerable structural homology to a fatty acid binding domain. Further analysis of the structure revealed a metal binding site, shown unambiguously to specifically bind zinc via a nonclassical, potentially catalytic zinc-binding motif. Based on the structural homology of the HEV protein with known structures, along with the presence of a catalytic zinc-binding motif, it is possible that the identified protein corresponds to the HEV protease, which could require activation or repression through the binding of a fatty acid. This represents a significant step forward in the characterization and the understanding of the molecular mechanisms of the HEV genome. We present analysis for the first time of this identified nonstructural protein, expanding the knowledge and understanding of the complex mechanisms of HEV biology.IMPORTANCE Hepatitis E virus (HEV) is an emerging virus found predominately in developing countries; it causes an estimated 20 million infections, which result in approximately 57,000 deaths a year. Although it is known that the nonstructural proteins of HEV ORF1 are expressed as a single transcript, there is debate as to whether ORF1 functions as a single polyprotein or if it is processed into separate domains via a viral or endogenous cellular protease. Here we present the first structural and biophysical characterization of an HEV nonstructural protein using a construct that has partially overlapping boundaries with the predicted putative cysteine protease.

Dataset Information

Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution.

Publications

Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets