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    slyD FKBP-type peptidyl-prolyl cis-trans isomerase SlyD [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 947859, updated on 3-Dec-2024

    Summary

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    Official Symbol
    slyD
    Official Full Name
    FKBP-type peptidyl-prolyl cis-trans isomerase SlyD
    Primary source
    ECOCYC:EG11663
    Locus tag
    b3349
    See related
    ASAP:ABE-0010946
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
    Lineage
    Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
    Also known as
    ECK3336
    Summary
    HypB requires binding of SlyD for hydrogenase activity as SlyD helps facilitate nickel insertion. [More information is available at EcoGene: EG11663]. SlyD is a peptidyl prolyl cis/trans-isomerase (PPIase) and chaperone. [More information is available at EcoCyc: EG11663].
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    Genomic context

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    Sequence:
    NC_000913.3 (3477907..3478497, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene peptidyl-prolyl cis-trans isomerase FkpA Neighboring gene protein SlyX Neighboring gene DUF2387 domain-containing protein YheV Neighboring gene K(+) : H(+) antiporter KefB Neighboring gene glutathione-regulated potassium-efflux system ancillary protein KefG

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_000913.3

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Positive charges promote the recognition of proteins by the chaperone SlyD from Escherichia coli. Lindemeier D, et al. PLoS One, 2024. PMID 38917203, Free PMC Article
    2. Two-step method to isolate target recombinant protein from co-purified bacterial contaminant SlyD after immobilised metal affinity chromatography. Parsy CB, et al. J Chromatogr B Analyt Technol Biomed Life Sci, 2007 Jun 15. PMID 17459787
    3. The peptidyl-prolyl isomerase activity of SlyD is not required for maturation of Escherichia coli hydrogenase. Zhang JW, et al. J Bacteriol, 2007 Nov. PMID 17720786, Free PMC Article
    4. Solubilization of aggregation-prone heterologous proteins by covalent fusion of stress-responsive Escherichia coli protein, SlyD. Han KY, et al. Protein Eng Des Sel, 2007 Nov. PMID 17971396
    5. Consequences of domain insertion on the stability and folding mechanism of a protein. Zoldák G, et al. J Mol Biol, 2009 Mar 6. PMID 19136015

    See all (58) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Positive charges promote the recognition of proteins by the chaperone SlyD from Escherichia coli.
      Title: Positive charges promote the recognition of proteins by the chaperone SlyD from Escherichia coli.
    2. Metal specificity of the Ni(II) and Zn(II) binding sites of the N-terminal and G-domain of E. coli HypB.
      Title: Metal specificity of the Ni(II) and Zn(II) binding sites of the N-terminal and G-domain of E. coli HypB.
    3. YdiV regulates Escherichia coli ferric uptake by manipulating the DNA-binding ability of Fur in a SlyD-dependent manner.
      Title: YdiV regulates Escherichia coli ferric uptake by manipulating the DNA-binding ability of Fur in a SlyD-dependent manner.
    4. SlyD has an essential role in the generation of the fully cofactor-equipped hydrogenase large subunits in the stationary phase where the level of each Hyd enzyme is finely tuned by SlyD for optimal enzyme activity
      Title: SlyD-dependent nickel delivery limits maturation of [NiFe]-hydrogenases in late-stationary phase Escherichia coli cells.
    5. the importance of the unusual metal-binding domain of E. coli SlyD in hydrogenase biogenesis
      Title: Nickel binding and [NiFe]-hydrogenase maturation by the metallochaperone SlyD with a single metal-binding site in Escherichia coli.
    6. Data support model in which HypB-SlyD complex establishes communication between GTP hydrolysis and nickel delivery and provide insight into role of HypB-SlyD complex during [NiFe]-hydrogenase biosynthesis.
      Title: Escherichia coli SlyD, more than a Ni(II) reservoir.
    7. the metal selectivity of SlyD
      Title: Metal selectivity of the Escherichia coli nickel metallochaperone, SlyD.
    8. Unfolded protein molecules initially form a highly dynamic complex with the chaperone domain of SlyD, and they are then transferred to the prolyl isomerase domain.
      Title: Cooperation of the prolyl isomerase and chaperone activities of the protein folding catalyst SlyD.
    9. On the basis of the presented data a model for nickel binding to SlyD as well as its role in nickel homeostasis is discussed.
      Title: The Ni(II)-binding properties of the metallochaperone SlyD.
    10. N-terminus verified by Edman degradation on complete protein
      Title: The Escherichia coli SlyD is a metal ion-regulated peptidyl-prolyl cis/trans-isomerase.
    Submit: New GeneRIF Correction See all GeneRIFs (14)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    enables RNA polymerase II CTD heptapeptide repeat P3 isomerase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II CTD heptapeptide repeat P6 isomerase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cobalt ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables copper ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nickel cation binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables peptidyl-prolyl cis-trans isomerase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables peptidyl-prolyl cis-trans isomerase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables peptidyl-prolyl cis-trans isomerase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables peptidyl-prolyl cis-trans isomerase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables unfolded protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein maturation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein maturation by protein folding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein refolding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein refolding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein refolding IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within protein stabilization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within response to heat IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    FKBP-type peptidyl-prolyl cis-trans isomerase SlyD
    NP_417808.1

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_000913.3 Reference assembly

      Range
      3477907..3478497 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_417808.1 FKBP-type peptidyl-prolyl cis-trans isomerase SlyD [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_417808.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A3L5H1N3
      Conserved Domains (1) summary
      PRK10737
      Location:1 → 196
      PRK10737; peptidylprolyl isomerase
    Nucleotide Protein
    Heading Accession and Version

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