P0A9K9 · SLYD_ECOLI

  • Protein
    FKBP-type peptidyl-prolyl cis-trans isomerase SlyD
  • Gene
    slyD
  • Status
    UniProtKB reviewed (Swiss-Prot)
  • Amino acids
  • Protein existence
    Evidence at protein level
  • Annotation score
    5/5

Function

function

Folding helper with both chaperone and peptidyl-prolyl cis-trans isomerase (PPIase) activities. Chaperone activity prevents aggregation of unfolded or partially folded proteins and promotes their correct folding. PPIases catalyze the cis-trans isomerization of Xaa-Pro bonds of peptides, which accelerates slow steps of protein folding and thus shortens the lifetime of intermediates. Both strategies lower the concentration of intermediates and increase the productivity and yield of the folding reaction. SlyD could be involved in Tat-dependent translocation, by binding to the Tat-type signal of folded proteins. The PPIase substrate specificity, carried out with synthetic peptides of the 'suc-Ala-Xaa-Pro-Phe-4NA' type (where Xaa is the AA tested), was found to be Phe > Ala > Leu.
Required for lysis of phiX174 infected cells by stabilizing the hydrophobic viral lysis protein E and allowing it to accumulate to the levels required to exert its lytic effect. May act by a chaperone-like mechanism.
Also involved in hydrogenase metallocenter assembly, probably by participating in the nickel insertion step. This function in hydrogenase biosynthesis requires chaperone activity and the presence of the metal-binding domain, but not PPIase activity.

Miscellaneous

The activity of SlyD is considerably smaller than the one found in other PPIases with the same substrate.

Catalytic activity

Activity regulation

PPIase activity is inhibited by binding of nickel ions to the C-terminal metal-binding region and/or the C-terminal part of the PPIase domain. Folding activity is inhibited by FK506 and by permanently unfolded proteins, irrespective of their proline content.

Features

Showing features for binding site.

TypeIDPosition(s)Description
Binding site167Ni2+ (UniProtKB | ChEBI)
Binding site168Ni2+ (UniProtKB | ChEBI)
Binding site184Ni2+ (UniProtKB | ChEBI)
Binding site185Ni2+ (UniProtKB | ChEBI)
Binding site193Ni2+ (UniProtKB | ChEBI)
Binding site195Ni2+ (UniProtKB | ChEBI)

GO annotations

AspectTerm
Cellular Componentcytosol
Molecular Functioncobalt ion binding
Molecular Functioncopper ion binding
Molecular Functionnickel cation binding
Molecular Functionpeptidyl-prolyl cis-trans isomerase activity
Molecular Functionunfolded protein binding
Molecular Functionzinc ion binding
Biological Processprotein maturation
Biological Processprotein maturation by protein folding
Biological Processprotein refolding
Biological Processprotein stabilization
Biological Processresponse to heat

Keywords

Enzyme and pathway databases

Names & Taxonomy

Protein names

  • Recommended name
    FKBP-type peptidyl-prolyl cis-trans isomerase SlyD
  • EC number
  • Short names
    PPIase
  • Alternative names
    • Histidine-rich protein
    • Metallochaperone SlyD
    • Rotamase
    • Sensitivity to lysis protein D
    • WHP

Gene names

    • Name
      slyD
    • Ordered locus names
      b3349, JW3311

Organism names

  • Taxonomic identifier
  • Strains
    • K12 / ATCC 35607 / JM83
    • K12 / CS109
    • K12 / MG1655 / ATCC 47076
    • K12 / W3110 / ATCC 27325 / DSM 5911
    • BL21
    • K12 / MC4100 / JA176
  • Taxonomic lineage
    Bacteria > Pseudomonadota > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Escherichia

Accessions

  • Primary accession
    P0A9K9
  • Secondary accessions
    • P30856
    • Q2M714

Proteomes

Subcellular Location

Keywords

Phenotypes & Variants

Disruption phenotype

Cells undergo an apoptotic-like death upon DNA damage characterized by membrane depolarization.

Features

Showing features for mutagenesis.

TypeIDPosition(s)Description
Mutagenesis42Decrease in PPIase activity, but has little impact on chaperone activity and interaction with HypB. Almost complete loss of PPIase activity; when associated with Y-132.
Mutagenesis132Almost complete loss of PPIase activity, but has little impact on chaperone activity and interaction with HypB; when associated with S-42.
Mutagenesis167-168Reduces nickel-binding capacity.
Mutagenesis184-185Reduces nickel-binding capacity.

PTM/Processing

Features

Showing features for chain.

TypeIDPosition(s)Description
ChainPRO_00000753551-196FKBP-type peptidyl-prolyl cis-trans isomerase SlyD

Proteomic databases

Interaction

Subunit

Monomer. Binds to a broad range of unrelated Tat signal sequences. Interacts with the hydrogenase nickel incorporation protein HypB.
(Microbial infection) Interacts with Enterobacteria phage phiX174 lysis protein E; this interaction protects E from proteolysis and stabilizes the YES complex (PubMed:37440661).
Part of the YES complex composed of 2 host Mray molecules, 2 viral lysis protein E molecules and 2 host SlyD molecules (PubMed:37440661).

Binary interactions

TypeEntry 1Entry 2Number of experimentsIntact
BINARY P0A9K9grcA P680663EBI-369251, EBI-561424
BINARY P0A9K9hycE P164317EBI-369251, EBI-552702
BINARY P0A9K9hypB P0AAN36EBI-369251, EBI-558261

Protein-protein interaction databases

Family & Domains

Features

Showing features for region, domain.

TypeIDPosition(s)Description
Region1-69PPIase first part
Domain1-95PPIase FKBP-type
Region76-120IF-chaperone
Region129-151PPIase second part

Domain

The N-terminal region consists of two globular folded domains that contain prolyl isomerase and chaperone activities.
The C-terminal region binds up to 7 nickel ions in a non-cooperative manner. Can also bind zinc with high affinity, and copper or cobalt with lower affinity. No binding detectable for ferrous, ferric, magnesium and calcium ions. Binding of nickel causes conformational rearrangements in the PPIase domain, modulating its isomerase activity. This region is also important for hydrogenase biosynthesis.

Sequence similarities

Belongs to the FKBP-type PPIase family.

Phylogenomic databases

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Length
    196
  • Mass (Da)
    20,853
  • Last updated
    2005-07-19 v1
  • Checksum
    46DCC7C7ECD61DBA
MKVAKDLVVSLAYQVRTEDGVLVDESPVSAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENLVQRVPKDVFMGVDELQVGMRFLAETDQGPVPVEITAVEDDHVVVDGNHMLAGQNLKFNVEVVAIREATEEELAHGHVHGAHDHHHDHDHDGCCGGHGHDHGHEHGGEGCCGGKGNGGCGCH

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
Z21496
EMBL· GenBank· DDBJ
CAA79705.1
EMBL· GenBank· DDBJ
Genomic DNA
L13261
EMBL· GenBank· DDBJ
AAA18574.1
EMBL· GenBank· DDBJ
Unassigned DNA
L28082
EMBL· GenBank· DDBJ
AAC41458.1
EMBL· GenBank· DDBJ
Genomic DNA
U18997
EMBL· GenBank· DDBJ
AAA58146.1
EMBL· GenBank· DDBJ
Genomic DNA
U00096
EMBL· GenBank· DDBJ
AAC76374.1
EMBL· GenBank· DDBJ
Genomic DNA
AP009048
EMBL· GenBank· DDBJ
BAE77942.1
EMBL· GenBank· DDBJ
Genomic DNA

Genome annotation databases

Similar Proteins

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