Comparative Protein Modeling Research Articles

Molecular structure, expression and bioactivity characterization of TNF13B (BAFF) gene in mefugu, Takifugu obscurus

B-cell activating factor of the TNF family (BAFF) induces B-cell survival, proliferation, immunoglobulin secretion and plays a role in enhancing immune responses. In the present study, a BAFF homolog has been identified in mefugu Takifugu obscurus, and its biological activities have been characterized. The mefugu BAFF (fBAFF) cDNA is 789 bp in length and translates into a 262-aa protein. The fBAFF genomic sequence consists of six exons and five introns, is approximately 1.8 kb in size. Amino acid sequence comparison indicated that fBAFF possessed the TNF signatures, a transmembrane domain, a putative furin protease cleavage site and three cysteine residues, which were the typical characteristics of TNF gene in mammals and birds. The predicted three-dimensional (3D) structure of the fsBAFF monomer analyzed by comparative protein modeling revealed that it was very similar to its human counterpart. Real-time quantitative PCR (qPCR) analysis revealed that fBAFF was predominantly expressed in mefugu lymphoid tissue spleen. The SUMO-fsBAFF and GFP/fsBAFF efficiently expressed in Escherichia coli Rosetta (DE3) were confirmed by SDS-PAGE and Western blotting analysis. After purification, the GFP/fsBAFF fusion protein obtained similar fluorescence spectrum to those of GFP. Laser scanning confocal microscopy analysis showed GFP/fsBAFF could bind to its receptors. In vitro, the MTT assays and flow cytometric analysis indicated that SUMO-fsBAFF could promote the proliferation of mefugu splenocytes or mouse splenic B cells together with/without anti-mouse IgM. These findings indicate that SUMO-fsBAFF plays an important role in proliferation of mefugu B cells and has functional cross-reactivity among mefugu and other mammalians. Therefore, BAFF may be a potential immunologic factor for enhancing immunological efficacy in fish.

Validation of Arsenic Resistance in Bacillus cereus Strain AG27 by Comparative Protein Modeling of arsC Gene Product

The ars gene system provides arsenic resistance to a variety of microorganisms and can be chromosomal or plasmid-borne. The arsC gene, which codes for an arsenate reductase is essential for arsenate resistance and transforms arsenate into arsenite, which is extruded from the cell. Therefore, arsC gene from Bacillus cereus strain AG27 isolated from soil was amplified, cloned and sequenced. The strain exhibited a minimum inhibitory concentration of 40 and 35mM to sodium arsenate and sodium arsenite, respectively. Homology of the sequence, when compared with available database using BLASTn search showed that 300bp amplicons obtained possess partial arsC gene sequence which codes for arsenate reductase, an enzyme involved in the reduction of arsenate to arsenite which is then effluxed out of the cell, thereby indicating the presence of efflux mechanism of resistance in strain. The efflux mechanism was further confirmed by atomic absorption spectroscopy and scanning electron microscopy studies. Moreover, three dimensional structure of modeled arsC from Bacillus cereus strain shares significant structural similarity with arsenate reductase protein of B.subtilis, consisting of, highly similar overall fold with single α/β domain containing a central four stranded, parallel, open-twisted β-sheet flanked by α-helices on both sides. The structure harbors the arsenic binding motif AB loop or P-loop that is highly conserved in arsenate reductase family.

RNA channelling by the eukaryotic exosome

The eukaryotic exosome is a key nuclease for the degradation, processing and quality control of a wide variety of RNAs. Here, we report electron microscopic reconstructions and pseudo-atomic models of the ten-subunit Saccharomyces cerevisiae exosome in the unbound and RNA-bound states. In the RNA-bound structures, extra density that is visible at the entry and exit sites of the exosome channel indicates that a substrate-threading mechanism is used by the eukaryotic exosome. This channelling mechanism seems to be conserved in exosome-like complexes from all domains of life, and might have been present in the most recent common ancestor.

Missing Value Estimation for Compound-Target Activity Data.

Relationships between drug targets and associated diseases have traditionally been investigated by means of sequence similarity, comparative protein modeling, and pathway analysis. Recently, a complementary paradigm has emerged to link targets and drugs via biological responses within activity data and visualize findings in networks. It has been indicated that one of the obstacles towards the identification of novel interactions is the sparsity of available data. In this article, we provide a survey of estimation methods that address the challenge of data sparsity. Each method is described in terms of its advantages and limitations, and an exemplary application on compound-target activity data is demonstrated. With such imputation methods in-hand, the opportunity to combine efforts in molecular informatics can be realized, yielding novel insights into ligand-target space.

Adhesion, Invasion, and Agglutination Mediated by Two Trimeric Autotransporters in the Human Uropathogen Proteus mirabilis

Fimbriae of the human uropathogen Proteus mirabilis are the only characterized surface proteins that contribute to its virulence by mediating adhesion and invasion of the uroepithelia. PMI2122 (AipA) and PMI2575 (TaaP) are annotated in the genome of strain HI4320 as trimeric autotransporters with "adhesin-like" and "agglutinating adhesin-like" properties, respectively. The C-terminal 62 amino acids (aa) in AipA and 76 aa in TaaP are homologous to the translocator domains of YadA from Yersinia enterocolitica and Hia from Haemophilus influenzae. Comparative protein modeling using the Hia three-dimensional structure as a template predicted that each of these domains would contain four antiparallel beta sheets and that they formed homotrimers. Recombinant AipA and TaaP were seen as ∼28 kDa and ∼78 kDa, respectively, in Escherichia coli, and each also formed high-molecular-weight homotrimers, thus supporting this model. E. coli synthesizing AipA or TaaP bound to extracellular matrix proteins with a 10- to 60-fold-higher level of affinity than the control strain. Inactivation of aipA in P. mirabilis strains significantly (P < 0.01) reduced the mutants' ability to adhere to or invade HEK293 cell monolayers, and the functions were restored upon complementation. A 51-aa-long invasin region in the AipA passenger domain was required for this function. E. coli expressing TaaP mediated autoagglutination, and a taaP mutant of P. mirabilis showed significantly (P < 0.05) more reduced aggregation than HI4320. Gly-247 in AipA and Gly-708 in TaaP were indispensable for trimerization and activity. AipA and TaaP individually offered advantages to P. mirabilis in a murine model. This is the first report characterizing trimeric autotransporters in P. mirabilis as afimbrial surface adhesins and autoagglutinins.

Molecular structure, expression, cell and tissue distribution, immune evolution and cell proliferation of the gene encoding bovine ( Bos taurus) TNFSF13 (APRIL)

A novel bovine cDNA has been isolated by EST assembly and subsequently confirmed by using RT-PCR and designated bovine A Proliferation-Inducing Ligand belonging to TNF family (bAPRIL). The open reading frame (ORF) of this cDNA covers 753 bp, encoding 250 amino acids. The functional soluble part of bAPRIL (bsAPRIL) shows 97% and 92% identity with its pig and human counterparts, respectively, at the level of the primary protein structure. The bAPRIL genomic sequence consists of six exons and five introns, is approximately 1.8 kb in size, and maps to bovine chromosome 19q. Real-time quantitative PCR (qPCR) analysis revealed that bAPRIL is predominantly expressed in bovine lymphoid tissues spleen. The predicted three-dimensional (3D) structure of the bsAPRIL monomer analyzed by “comparative protein modelling” revealed that it is very similar to its mouse counterpart. The bsAPRIL and EGFP/bsAPRIL were efficiently expression in Escherichia coli BL21 (DE3) and its expression was confirmed by SDS-PAGE and Western blotting analysis. After purification, the EGFP/bsAPRIL fusion protein obtained similar fluorescence spectrum to those of EGFP. Laser scanning confocal microscopy analysis showed EGFP/bsAPRIL could bind to its receptor. In vitro, bsAPRIL could promote the proliferation of bovine or mouse splenic B cells together with/without SAC or anti-mouse IgM. Furthermore, compared to mouse soluble APRIL, the bovine soluble APRIL has the similar proliferation to mouse B cell. Those findings indicated that bsAPRIL plays an important role in proliferation of bovine B cells and has functional cross-reactivity among cow and other mammalians. Therefore, APRIL may be a potential immunologic factor for enhancing immunological efficacy in animals.

Cloning, expression and bioactivity of BAFF from Petaurus breviceps

B-cell activating factor (BAFF), belonging to the TNF (tumor necrosis factor) family, is crucial for B-cell survival and maturation. In the present study, PbBAFF cDNA was amplified from the sugar glider Petaurus breviceps by RT-PCR and RACE (rapid amplification of cDNA ends) strategies. The open reading frame (ORF) of PbBAFF cDNA encodes a protein consisting of 287-amino acid. The deduced amino acid sequence contains a predicted transmembrane domain, a putative furin protease cleavage site, a potential N-glycosylation site and conserved cysteine residues similar to that identified in other mammalian BAFF. The soluble mature part of PbBAFF (PbsBAFF) showed 88–92% sequence identity with mammalian homologs. The predicted three-dimensional (3D) structural analysis of PbsBAFF analyzed by comparative protein modeling revealed that they are very similar to the 3D structure of human BAFF. Recombinant PbsBAFF fused with His 6 tag was efficiently expressed in Escherichia coli BL21 (DE3). In vitro, purified PbsBAFF co-stimulates the proliferation of human B-cells. These findings indicate PbBAFF, the first BAFF cloned from marsupial, plays an important role in proliferation of B-cells, and phylogenetic analyses reveal that the work is of value with respect to continued refinement of our understanding of mammalian phylogenetic relationships.

TRACER. A new approach to comparative modeling that combines threading with free-space conformational sampling.

A new approach to comparative modeling of proteins, TRACER, is described and benchmarked against classical modeling procedures. The new method unifies true three-dimensional threading with coarse-grained sampling of query protein conformational space. The initial sequence alignment of a query protein with a template is not required, although a template needs to be somehow identified. The template is used as a multi-featured fuzzy three-dimensional scaffold. The conformational search for the query protein is guided by intrinsic force field of the coarse-grained modeling engine CABS and by compatibility with the template scaffold. During Replica Exchange Monte Carlo simulations the model chain representing the query protein finds the best possible structural alignment with the template chain, that also optimizes the intra-protein interactions as approximated by the knowledge based force field of CABS. The benchmark done for a representative set of query/template pairs of various degrees of sequence similarity showed that the new method allows meaningful comparative modeling also for the region of marginal, or non-existing, sequence similarity. Thus, the new approach significantly extends the applicability of comparative modeling.

Detection of mutations in the FemXAB protein family in oxacillin-susceptible mecA-positive Staphylococcus aureus clinical isolates

Objectives Methicillin-resistant Staphylococcus aureus (MRSA) strains that express the mecA gene but are oxacillin susceptible (OS-MRSA; oxacillin MIC </=2 mg/L) are increasingly reported. To gain molecular and functional insights on this observation, we focused on additional factors possibly contributing to phenotypic susceptibility. Methods The nucleotide content of mecA, femA, femB and femX genes, which are considered essential for methicillin resistance, was determined in four OS-MRSA clinical isolates and a genetically similar low-level MRSA control (oxacillin MIC 6 mg/L). Gene expression was quantified compared with the low- and a high-level MRSA (MIC 256 mg/L) control. The tertiary structure of Fem proteins was predicted based on protein structure homology modelling, using web-based automated comparative protein modelling. Growth kinetics were tested for the study and control isolates, to determine whether FemXAB mutations lead to reduced fitness. Results Genes mecA, femA, femB and femX were expressed similarly in the study and the control isolates. Mutations in the gene mecA were not present in any isolate. However, several mutations leading to amino acid substitutions in positions possibly affecting Fem enzyme activity were detected in all fem genes. Two OS-MRSA that had no oxacillin heteroresistance had more mutations in the Fem proteins compared with the remaining isolates that were heteroresistant. The low-level MRSA control had considerably fewer mutations. No differences between growth rates of the OS-MRSA and the MRSA controls were observed. Conclusions Accumulation of amino acid changes in Fem proteins might affect intact cell wall synthesis, even though not causing reduced viability, thus contributing to atypical oxacillin responsiveness.

Unraveling the molecular mechanisms of nitrogenase conformational protection against oxygen in diazotrophic bacteria

BackgroundG. diazotrophicus and A. vinelandii are aerobic nitrogen-fixing bacteria. Although oxygen is essential for the survival of these organisms, it irreversibly inhibits nitrogenase, the complex responsible for nitrogen fixation. Both microorganisms deal with this paradox through compensatory mechanisms. In A. vinelandii a conformational protection mechanism occurs through the interaction between the nitrogenase complex and the FeSII protein. Previous studies suggested the existence of a similar system in G. diazotrophicus, but the putative protein involved was not yet described. This study intends to identify the protein coding gene in the recently sequenced genome of G. diazotrophicus and also provide detailed structural information of nitrogenase conformational protection in both organisms.ResultsGenomic analysis of G. diazotrophicus sequences revealed a protein coding ORF (Gdia0615) enclosing a conserved “fer2” domain, typical of the ferredoxin family and found in A. vinelandii FeSII. Comparative models of both FeSII and Gdia0615 disclosed a conserved beta-grasp fold. Cysteine residues that coordinate the 2[Fe-S] cluster are in conserved positions towards the metallocluster. Analysis of solvent accessible residues and electrostatic surfaces unveiled an hydrophobic dimerization interface. Dimers assembled by molecular docking presented a stable behaviour and a proper accommodation of regions possibly involved in binding of FeSII to nitrogenase throughout molecular dynamics simulations in aqueous solution. Molecular modeling of the nitrogenase complex of G. diazotrophicus was performed and models were compared to the crystal structure of A. vinelandii nitrogenase. Docking experiments of FeSII and Gdia0615 with its corresponding nitrogenase complex pointed out in both systems a putative binding site presenting shape and charge complementarities at the Fe-protein/MoFe-protein complex interface.ConclusionsThe identification of the putative FeSII coding gene in G. diazotrophicus genome represents a large step towards the understanding of the conformational protection mechanism of nitrogenase against oxygen. In addition, this is the first study regarding the structural complementarities of FeSII-nitrogenase interactions in diazotrophic bacteria. The combination of bioinformatic tools for genome analysis, comparative protein modeling, docking calculations and molecular dynamics provided a powerful strategy for the elucidation of molecular mechanisms and structural features of FeSII-nitrogenase interaction.

Template-Based Protein Modeling: Recent Methodological Advances

Protein modeling has been a very challenging problem in drug discovery and computational biology. The latest advances and progress in computational power have helped to solve this problem to a considerable extent; however, predicting accurate three-dimensional structure of proteins has always been and remains a complicated assignment. Of the two common methods of protein structure prediction, template-based modeling has become more popular than ab initio modeling. In this review, we summarize the developments in methodology and of understanding for comparative protein modeling during the last three years, including for homologue search, fold recognition, secondary structure prediction, model building, loop building, side-chain prediction and model quality assessment.

Comparative Protein Modeling, Prediction of Conserved Residue and Active Sites in Cold Resistant Protein Isolated from CRPF1, A Cold Tolerant Mutant of Pseudomonas fluorescens

Proteins interacting with the biological information molecules DNA and RNA play important cellular roles in all organisms. One widespread super family of proteins implicated in such function(s) is cold shock protein (CSP) that contains the cold shock domain (CSD). This work is planned to study the three-dimensional structure, conserved residues, and different active sites in the structure of cold resistant protein (CRP) from CRPF(1), cold tolerant mutant of Pseudomonas fluorescence by comparative homology modeling. Here we tried to identify crucial residues that are involved in active sites or functional sites of the protein. The study reveals that CRP represent the prototype of the CSD and share a highly similar overall fold consisting of five antiparallel beta-sheets forming a beta-barrel structure with surface exposed aromatic and basic residues that were responsible for nucleic acid binding properties of variable binding affinities and sequence selectivity and harbors the nucleic acid binding motifs RNP1 and RNP2 that is highly conserved in CSP family.

GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains

GeMMA (Genome Modelling and Model Annotation) is a new approach to automatic functional subfamily classification within families and superfamilies of protein sequences. A major advantage of GeMMA is its ability to subclassify very large and diverse superfamilies with tens of thousands of members, without the need for an initial multiple sequence alignment. Its performance is shown to be comparable to the established high-performance method SCI-PHY. GeMMA follows an agglomerative clustering protocol that uses existing software for sensitive and accurate multiple sequence alignment and profile–profile comparison. The produced subfamilies are shown to be equivalent in quality whether whole protein sequences are used or just the sequences of component predicted structural domains. A faster, heuristic version of GeMMA that also uses distributed computing is shown to maintain the performance levels of the original implementation. The use of GeMMA to increase the functional annotation coverage of functionally diverse Pfam families is demonstrated. It is further shown how GeMMA clusters can help to predict the impact of experimentally determining a protein domain structure on comparative protein modelling coverage, in the context of structural genomics.

Automated comparative protein structure modeling with SWISS‐MODEL and Swiss‐PdbViewer: A historical perspective

SWISS-MODEL pioneered the field of automated modeling as the first protein modeling service on the Internet. In combination with the visualization tool Swiss-PdbViewer, the Internet-based Workspace and the SWISS-MODEL Repository, it provides a fully integrated sequence to structure analysis and modeling platform. This computational environment is made freely available to the scientific community with the aim to hide the computational complexity of structural bioinformatics and encourage bench scientists to make use of the ever-increasing structural information available. Indeed, over the last decade, the availability of structural information has significantly increased for many organisms as a direct consequence of the complementary nature of comparative protein modeling and experimental structure determination. This has a very positive and enabling impact on many different applications in biomedical research as described in this paper.

A Kernel for Open Source Drug Discovery in Tropical Diseases

BackgroundConventional patent-based drug development incentives work badly for the developing world, where commercial markets are usually small to non-existent. For this reason, the past decade has seen extensive experimentation with alternative R&D institutions ranging from private–public partnerships to development prizes. Despite extensive discussion, however, one of the most promising avenues—open source drug discovery—has remained elusive. We argue that the stumbling block has been the absence of a critical mass of preexisting work that volunteers can improve through a series of granular contributions. Historically, open source software collaborations have almost never succeeded without such “kernels”.Methodology/Principal FindingsHere, we use a computational pipeline for: (i) comparative structure modeling of target proteins, (ii) predicting the localization of ligand binding sites on their surfaces, and (iii) assessing the similarity of the predicted ligands to known drugs. Our kernel currently contains 143 and 297 protein targets from ten pathogen genomes that are predicted to bind a known drug or a molecule similar to a known drug, respectively. The kernel provides a source of potential drug targets and drug candidates around which an online open source community can nucleate. Using NMR spectroscopy, we have experimentally tested our predictions for two of these targets, confirming one and invalidating the other.Conclusions/SignificanceThe TDI kernel, which is being offered under the Creative Commons attribution share-alike license for free and unrestricted use, can be accessed on the World Wide Web at http://www.tropicaldisease.org. We hope that the kernel will facilitate collaborative efforts towards the discovery of new drugs against parasites that cause tropical diseases.

ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI)

John Overington holds a first degree in chemistry, and studied for his PhD on comparative protein modeling, drug design, and sequence-structure relationships with Sir Tom Blundell FRS, at Birkbeck College, London. After a postdoctoral fellowship with the Imperial Cancer Research Fund, London, he joined Pfizer Central Research in the UK and eventually became manager of the Molecular Informatics, Structure and Design Department, where he was responsible for cheminformatics, structural biology, target analysis, and molecular modeling. He joined Inpharmatica in 2000; Inpharmatica was acquired by Galapagos NV in December 2006. There he was Senior Director, Discovery Informatics of the Galapagos subsidiary BioFocus DPI. In October 2008 he was appointed Team Leader, Chemogenomics at the European Molecular Biology Laboratory (EMBL), working at the European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK. His ChEMBL group’s research focuses on mapping the interactions and functional effects of small molecules binding to their macromolecular targets. The group studies the interactions of pharmacologically active molecules and their receptors. In particular it builds and maintains a series of large-scale drug discovery databases, known collectively as ChEMBL. Interview

Refinement Of Protein Model Structures In Explicit Solvent Using Biasing Potential Replica Exchange Simulations

Comparative protein modeling of a target protein based on sequence similarity to a protein with known structure is widely used to provide structural models of proteins. Frequently, the quality of the target- template sequence alignment is non-uniform along the sequence: parts can be modeled with a high confidence, whereas other parts differ strongly from the template. In principle, molecular dynamics (MD) simulations can be used to refine protein model structures but it is limited by the currently accessible simulation time scales. We have used a recently developed biasing potential replica exchange (BP-Rex) MD method (Kannan, S. Zacharias, M. Proteins 2007, 66, 697-70) to refine homology modeled protein structure at atomic resolution including explicit solvent. In standard Rex-MD simulations several replicas of a system are run in parallel at different temperatures allowing exchanges at preset time intervals. In a BP-RexMD simulation replicas are controlled by various levels of a biasing potential to reduce the energy barriers associated with peptide backbone dihedral transitions. The method requires much fewer replicas for efficient sampling compared with standard temperature RexMD. It is also possible to focus the method to parts of a protein structure (segments of a model structure that may differ strongly from a template structure). Application to several protein structures indicates improved conformational sampling compared to conventional MD simulations. BP-RexMD simulations on several test cases starting from decoy structures deviating significantly from the native structure resulted in final structures in much closer agreement with experiment compared to conventional MD simulations.

Homology Modeling and Functional Analysis of LPG2 Protein of Leishmania Strains

As drug resistance problem persists in case of Leishmaniasis, modeling and analysis of different essential proteins of Leishmania strains will help us further to discover novel lead compounds. Lipophosphoglycan 2 (LPG2) protein is required for the development of Leishmania throughout their life cycle, including for virulence to the mammalian host. LPG2 participates in a specialized virulence pathway, which may offer an attractive target for chemotherapy. Homology models of LPG2 of five Leishmania species have been constructed using the X-ray structures of different transporter proteins as templates, by comparative protein modeling principles. The resulting model has the correct stereochemistry as gauged from the Ramachandran plot and good three-dimensional (3-D) structure compatibility as assessed by the Procheck and Profiles-3D scores. Functional assignment of LPG2 protein of Leishmania strains by SVM revealed that along with transporters activity it also performs several novel functions e.g. iron-binding, sodium-binding, copper binding. It also belongs to protein of major facilitator family (MFS) and type II (general) secretory pathway (IISP) family. Important functional motifs have been identified in LPG2 protein of different Leishmania strains using different programs. Potential Ligand Binding Sites (LBSs) in LPG2 protein of these strains have been identified using Pocket Finder program. On the basis of structure of ligand binding sites, particular LPG2 inhibitors can be designed. The similarity in the molecular structure, function and differences in LBSs of LPG2 of L. donovani, L. major, L. infantum, L. braziliensis and L. mexicana provide evidences for selective and specific LPG2 inhibitors.

AtNOS/AtNOA1 Is a Functional Arabidopsis thaliana cGTPase and Not a Nitric-oxide Synthase

AtNOS1 was previously identified as a potential nitric-oxide synthase (NOS) in Arabidopsis thaliana, despite lack of sequence similarity to animal NOSs. Although the dwarf and yellowish leaf phenotype of Atnos1 knock-out mutant plants can be rescued by treatment with exogenous NO, doubts have recently been raised as to whether AtNOS1 is a true NOS. Moreover, depending on the type of physiological responses studied, Atnos1 is not always deficient in NO induction and/or detection, as previously reported. Here, we present experimental evidence showing that AtNOS1 is unable to bind and oxidize arginine to NO. These results support the argument that AtNOS1 is not a NOS. We also show that the renamed NO-associated protein 1 (AtNOA1) is a member of the circularly permuted GTPase family (cGTPase). AtNOA1 specifically binds GTP and hydrolyzes it. Complementation experiments of Atnoa1 mutant plants with different constructs of AtNOA1 show that GTP hydrolysis is necessary but not sufficient for the physiological function of AtNOA1. Mutant AtNOA1 lacking the C-terminal domain, although retaining GTPase activity, failed to complement Atnoa1, suggesting that this domain plays a crucial role in planta. cGTPases appear to be RNA-binding proteins, and the closest homolog of AtNOA1, the Bacillus subtilis YqeH, has been shown to participate in ribosome assembly and stability. We propose a similar function for AtNOA1 and discuss it in the light of its potential role in NO accumulation and plant development.

Ethylmalonyl-CoA Mutase from Rhodobacter sphaeroides Defines a New Subclade of Coenzyme B12-dependent Acyl-CoA Mutases

Coenzyme B(12)-dependent mutases are radical enzymes that catalyze reversible carbon skeleton rearrangement reactions. Here we describe Rhodobacter sphaeroides ethylmalonyl-CoA mutase (Ecm), a novel member of the family of coenzyme B(12)-dependent acyl-CoA mutases, that operates in the recently discovered ethylmalonyl-CoA pathway for acetate assimilation. Ecm is involved in the central reaction sequence of this novel pathway and catalyzes the transformation of ethylmalonyl-CoA to methylsuccinyl-CoA in combination with a second enzyme that was further identified as promiscuous ethylmalonyl-CoA/methylmalonyl-CoA epimerase. In contrast to the epimerase, Ecm is highly specific for its substrate, ethylmalonyl-CoA, and accepts methylmalonyl-CoA only at 0.2% relative activity. Sequence analysis revealed that Ecm is distinct from (2R)-methylmalonyl-CoA mutase as well as isobutyryl-CoA mutase and defines a new subfamily of coenzyme B(12)-dependent acyl-CoA mutases. In combination with molecular modeling, two signature sequences were identified that presumably contribute to the substrate specificity of these enzymes.