Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria (Q34314123)

1 August 2017

title

Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria (English)

1 reference

1 August 2017

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Todd O Yeates

4

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author name string

Julien Jorda

series ordinal

1

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1 August 2017

David Lopez

series ordinal

2

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1 August 2017

Nicole M Wheatley

series ordinal

3

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1 August 2017

publication date

4 January 2013

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1 August 2017

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1 August 2017

volume

22

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1 August 2017

issue

2

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1 August 2017

page(s)

179-195

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Elucidating essential role of conserved carboxysomal protein CcmN reveals common feature of bacterial microcompartment assembly

1 August 2017

cites work

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Engineered protein nano-compartments for targeted enzyme localization

6 July 2018

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Transcriptional response of the sulfur chemolithoautotroph Thiomicrospira crunogena to dissolved inorganic carbon limitation

6 July 2018

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Isolation and characterization of the Prochlorococcus carboxysome reveal the presence of the novel shell protein CsoS1D.

6 July 2018

1 reference

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The N-terminal region of the medium subunit (PduD) packages adenosylcobalamin-dependent diol dehydratase (PduCDE) into the Pdu microcompartment

6 July 2018

1 reference

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HMMER web server: interactive sequence similarity searching

6 July 2018

1 reference

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Structural insights into radical generation by the radical SAM superfamily

6 July 2018

1 reference

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The protein shells of bacterial microcompartment organelles

6 July 2018

1 reference

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Structure of PduT, a trimeric bacterial microcompartment protein with a 4Fe-4S cluster-binding site

6 July 2018

1 reference

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Genetic analysis around aminoalcohol dehydrogenase gene of Rhodococcus erythropolis MAK154: a putative GntR transcription factor in transcriptional regulation

6 July 2018

1 reference

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Structural Insight into the Mechanisms of Transport across the Salmonella enterica Pdu Microcompartment Shell

6 July 2018

1 reference

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Bacterial Microcompartments

6 July 2018

1 reference

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Synthesis of empty bacterial microcompartments, directed organelle protein incorporation, and evidence of filament-associated organelle movement.

6 July 2018

1 reference

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Addressing microbial organelles: a short peptide directs enzymes to the interior

6 July 2018

1 reference

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Short N-terminal sequences package proteins into bacterial microcompartments

6 July 2018

1 reference

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Ethanolamine utilization in bacterial pathogens: roles and regulation

6 July 2018

1 reference

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Bacterial microcompartment organelles: protein shell structure and evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Structural basis of the oxidative activation of the carboxysomal -carbonic anhydrase, CcmM

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Carboxysomal carbonic anhydrases: Structure and role in microbial CO2 fixation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Structure of a trimeric bacterial microcompartment shell protein, EtuB, associated with ethanol utilization in Clostridium kluyveri

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Crystal structure of the EutL shell protein of the ethanolamine ammonia lyase microcompartment

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Insights from multiple structures of the shell proteins from the β-carboxysome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Structural basis of enzyme encapsulation into a bacterial nanocompartment

6 July 2018

1 reference

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InterPro: the integrative protein signature database

6 July 2018

1 reference

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Bacterial microcompartments: their properties and paradoxes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Structure of the PduU shell protein from the Pdu microcompartment of Salmonella

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Ethanolamine activates a sensor histidine kinase regulating its utilization in Enterococcus faecalis

6 July 2018

1 reference

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Protein-based organelles in bacteria: carboxysomes and related microcompartments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Biochemical and structural insights into bacterial organelle form and biogenesis.

6 July 2018

1 reference

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The PduX enzyme of Salmonella enterica is an L-threonine kinase used for coenzyme B12 synthesis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Microcompartments for B12-dependent 1,2-propanediol degradation provide protection from DNA and cellular damage by a reactive metabolic intermediate

6 July 2018

1 reference

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Atomic-level models of the bacterial carboxysome shell

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

In silico characterization of proteins: UniProt, InterPro and Integr8.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

A multiprotein bicarbonate dehydration complex essential to carboxysome function in cyanobacteria

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Small multidrug resistance proteins: a multidrug transporter family that continues to grow.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Genomic and biochemical studies demonstrating the absence of an alkane-producing phenotype in Vibrio furnissii M1

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Self-assembly in the carboxysome: a viral capsid-like protein shell in bacterial cells.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

How electron cryotomography is opening a new window onto prokaryotic ultrastructure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

PduL is an evolutionarily distinct phosphotransacylase involved in B12-dependent 1,2-propanediol degradation by Salmonella enterica serovar typhimurium LT2.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Characterization of the carboxysomal carbonic anhydrase CsoSCA from Halothiobacillus neapolitanus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Free radical mechanisms in enzymology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Whole-genome transcription profiling reveals genes up-regulated by growth on fucose in the human gut bacterium "Roseburia inulinivorans"

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Radical enzymes in anaerobes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Conserving a volatile metabolite: a role for carboxysome-like organelles in Salmonella enterica

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Polyhedral organelles compartmenting bacterial metabolic processes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Minimal functions and physiological conditions required for growth of salmonella enterica on ethanolamine in the absence of the metabolosome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

New glycyl radical enzymes catalysing key metabolic steps in anaerobic bacteria

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Protein Structures Forming the Shell of Primitive Bacterial Organelles

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content

6 July 2018

1 reference

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The TetR family of transcriptional repressors.

6 July 2018

1 reference

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Phosphoryl transfer by aminoglycoside 3'-phosphotransferases and manifestation of antibiotic resistance

6 July 2018

1 reference

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Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary

6 July 2018

1 reference

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The new bacterial cell biology: moving parts and subcellular architecture

6 July 2018

1 reference

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Mechanism of cobyrinic acid a,c-diamide synthetase from Salmonella typhimurium LT2.

6 July 2018

1 reference

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Induction of a novel class of diacylglycerol acyltransferases and triacylglycerol accumulation in Mycobacterium tuberculosis as it goes into a dormancy-like state in culture

6 July 2018

1 reference

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Prolinks: a database of protein functional linkages derived from coevolution

6 July 2018

1 reference

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Mechanism of aromatic amino acid hydroxylation

6 July 2018

1 reference

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Enzymes with molecular tunnels

6 July 2018

1 reference

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CO2 concentrating mechanisms in cyanobacteria: molecular components, their diversity and evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Microcompartments in prokaryotes: carboxysomes and related polyhedra

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Carbamoyl phosphate synthetase: an amazing biochemical odyssey from substrate to product

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

The aromatic amino acid hydroxylases.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

A combined algorithm for genome-wide prediction of protein function

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

The propanediol utilization (pdu) operon of Salmonella enterica serovar Typhimurium LT2 includes genes necessary for formation of polyhedral organelles involved in coenzyme B(12)-dependent 1, 2-propanediol degradation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

The use of gene clusters to infer functional coupling

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Profile hidden Markov models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Propanediol utilization genes (pdu) of Salmonella typhimurium: three genes for the propanediol dehydratase

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Repression of the cob operon of Salmonella typhimurium by adenosylcobalamin is influenced by mutations in the pdu operon

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Selfish operons: horizontal transfer may drive the evolution of gene clusters

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Phenylalanine hydroxylase-stimulating protein/pterin-4 alpha-carbinolamine dehydratase from rat and human liver. Purification, characterization, and complete amino acid sequence

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

The MIP family of integral membrane channel proteins: sequence comparisons, evolutionary relationships, reconstructed pathway of evolution, and proposed functional differentiation of the two repeated halves of the proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

The control region of the pdu/cob regulon in Salmonella typhimurium

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Isolation and characterization of a carboxysome shell gene from Thiobacillus neapolitanus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Ethanolamine utilization in Salmonella typhimurium: nucleotide sequence, protein expression, and mutational analysis of the cchA cchB eutE eutJ eutG eutH gene cluster

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Taxonomic diversity of anaerobic glycerol dissimilation in the Enterobacteriaceae

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Five promoters integrate control of the cob/pdu regulon in Salmonella typhimurium

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Functional organelles in prokaryotes: polyhedral inclusions (carboxysomes) of Thiobacillus neapolitanus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

Autogenous regulation of ethanolamine utilization by a transcriptional activator of the eut operon in Salmonella typhimurium

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

The free radical in pyruvate formate-lyase is located on glycine-734

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588914

The novel genes, cbbQ and cbbO, located downstream from the RubisCO genes of Pseudomonas hydrogenothermophila, affect the conformational states and activity of RubisCO.

6 July 2018

1 reference

Phylogenomic and functional analysis of pterin-4a-carbinolamine dehydratase family (COG2154) proteins in plants and microorganisms.

21 January 2018

1 reference

The pyruvate formate lyase family: sequences, structures and activation

21 January 2018

1 reference

Insight into the mechanism of the B12-independent glycerol dehydratase from Clostridium butyricum: preliminary biochemical and structural characterization.

21 January 2018

1 reference

Organization of carboxysome genes in the thiobacilli

21 January 2018

1 reference

Identification and diversity of putative aminoglycoside-biosynthetic aminotransferase genes from deep-sea environmental DNA.

21 January 2018

1 reference

Identification of aminotransferase genes for biosynthesis of aminoglycoside antibiotics from soil DNA.

21 January 2018

1 reference

Ammonia channeling in bacterial glucosamine-6-phosphate synthase (Glms): molecular dynamics simulations and kinetic studies of protein mutants

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23188745

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The correlation of the gene csoS2 of the carboxysome operon with two polypeptides of the carboxysome in thiobacillus neapolitanus

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23188745

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PRO.2196

1 reference

1 August 2017

1 reference

1 August 2017

1 reference