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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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