P0A9K9 · SLYD_ECOLI
- ProteinFKBP-type peptidyl-prolyl cis-trans isomerase SlyD
- GeneslyD
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids196 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
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
- [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0)
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.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 167 | Ni2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 168 | Ni2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 184 | Ni2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 185 | Ni2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 193 | Ni2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 195 | Ni2+ (UniProtKB | ChEBI) | ||||
Sequence: C |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | cytosol | |
Molecular Function | cobalt ion binding | |
Molecular Function | copper ion binding | |
Molecular Function | nickel cation binding | |
Molecular Function | peptidyl-prolyl cis-trans isomerase activity | |
Molecular Function | unfolded protein binding | |
Molecular Function | zinc ion binding | |
Biological Process | protein maturation | |
Biological Process | protein maturation by protein folding | |
Biological Process | protein refolding | |
Biological Process | protein stabilization | |
Biological Process | response to heat |
Keywords
- Molecular function
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameFKBP-type peptidyl-prolyl cis-trans isomerase SlyD
- EC number
- Short namesPPIase
- Alternative names
Gene names
Organism names
- Organism
- Strains
- Taxonomic lineageBacteria > Pseudomonadota > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Escherichia
Accessions
- Primary accessionP0A9K9
- Secondary accessions
Proteomes
Subcellular Location
Phenotypes & Variants
Disruption phenotype
Cells undergo an apoptotic-like death upon DNA damage characterized by membrane depolarization.
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 42 | Decrease 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. | ||||
Sequence: I → S | ||||||
Mutagenesis | 132 | Almost complete loss of PPIase activity, but has little impact on chaperone activity and interaction with HypB; when associated with S-42. | ||||
Sequence: F → Y | ||||||
Mutagenesis | 167-168 | Reduces nickel-binding capacity. | ||||
Sequence: CC → AA | ||||||
Mutagenesis | 184-185 | Reduces nickel-binding capacity. | ||||
Sequence: CC → AA |
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000075355 | 1-196 | FKBP-type peptidyl-prolyl cis-trans isomerase SlyD | |||
Sequence: MKVAKDLVVSLAYQVRTEDGVLVDESPVSAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENLVQRVPKDVFMGVDELQVGMRFLAETDQGPVPVEITAVEDDHVVVDGNHMLAGQNLKFNVEVVAIREATEEELAHGHVHGAHDHHHDHDHDGCCGGHGHDHGHEHGGEGCCGGKGNGGCGCH |
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).
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
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | P0A9K9 | grcA P68066 | 3 | EBI-369251, EBI-561424 | |
BINARY | P0A9K9 | hycE P16431 | 7 | EBI-369251, EBI-552702 | |
BINARY | P0A9K9 | hypB P0AAN3 | 6 | EBI-369251, EBI-558261 |
Protein-protein interaction databases
Structure
Family & Domains
Features
Showing features for region, domain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Region | 1-69 | PPIase first part | ||||
Sequence: MKVAKDLVVSLAYQVRTEDGVLVDESPVSAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYG | ||||||
Domain | 1-95 | PPIase FKBP-type | ||||
Sequence: MKVAKDLVVSLAYQVRTEDGVLVDESPVSAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENLVQRVPKDVFMGVDELQVGMR | ||||||
Region | 76-120 | IF-chaperone | ||||
Sequence: VQRVPKDVFMGVDELQVGMRFLAETDQGPVPVEITAVEDDHVVVD | ||||||
Region | 129-151 | PPIase second part | ||||
Sequence: NLKFNVEVVAIREATEEELAHGH |
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 statusComplete
- Length196
- Mass (Da)20,853
- Last updated2005-07-19 v1
- Checksum46DCC7C7ECD61DBA
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
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 |