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Protein

FKBP-type peptidyl-prolyl cis-trans isomerase SlyD

Gene

slyD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.

Catalytic activityi

Peptidylproline (omega=180) = peptidylproline (omega=0).1 Publication

Enzyme regulationi

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.2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi167NickelSequence analysis1
Metal bindingi168NickelSequence analysis1
Metal bindingi184NickelSequence analysis1
Metal bindingi185NickelSequence analysis1
Metal bindingi193NickelSequence analysis1
Metal bindingi195NickelSequence analysis1

GO - Molecular functioni

  • cobalt ion binding Source: EcoCyc
  • copper ion binding Source: EcoCyc
  • FK506 binding Source: GO_Central
  • nickel cation binding Source: EcoCyc
  • peptidyl-prolyl cis-trans isomerase activity Source: EcoCyc
  • unfolded protein binding Source: EcoCyc
  • zinc ion binding Source: EcoCyc

GO - Biological processi

  • chaperone-mediated protein folding Source: GO_Central
  • protein maturation Source: EcoCyc
  • protein maturation by protein folding Source: EcoliWiki
  • protein refolding Source: EcoCyc
  • protein stabilization Source: EcoliWiki
  • response to heat Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Chaperone, Isomerase, Rotamase

Keywords - Ligandi

Cobalt, Copper, Metal-binding, Nickel, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG11663-MONOMER.
ECOL316407:JW3311-MONOMER.
MetaCyc:EG11663-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
FKBP-type peptidyl-prolyl cis-trans isomerase SlyD (EC:5.2.1.8)
Short name:
PPIase
Alternative name(s):
Histidine-rich protein
Metallochaperone SlyD
Rotamase
Sensitivity to lysis protein D
WHP
Gene namesi
Name:slyD
Ordered Locus Names:b3349, JW3311
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11663. slyD.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Cells undergo an apoptotic-like death upon DNA damage characterized by membrane depolarization.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi42I → S: 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. 1 Publication1
Mutagenesisi132F → Y: Almost complete loss of PPIase activity, but has little impact on chaperone activity and interaction with HypB; when associated with S-42. 1 Publication1
Mutagenesisi167 – 168CC → AA: Reduces nickel-binding capacity. 1 Publication2
Mutagenesisi184 – 185CC → AA: Reduces nickel-binding capacity. 1 Publication2

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000753551 – 196FKBP-type peptidyl-prolyl cis-trans isomerase SlyDAdd BLAST196

Proteomic databases

EPDiP0A9K9.
PaxDbiP0A9K9.
PRIDEiP0A9K9.

Interactioni

Subunit structurei

Monomer. Binds to a broad range of unrelated Tat signal sequences. Interacts with the hydrogenase nickel incorporation protein HypB.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
hycEP164317EBI-369251,EBI-552702
hypBP0AAN34EBI-369251,EBI-558261

GO - Molecular functioni

  • unfolded protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4260682. 10 interactors.
DIPiDIP-31853N.
IntActiP0A9K9. 119 interactors.
MINTiMINT-1223693.
STRINGi511145.b3349.

Structurei

Secondary structure

1196
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi7 – 17Combined sources11
Turni18 – 20Combined sources3
Beta strandi22 – 25Combined sources4
Beta strandi28 – 30Combined sources3
Beta strandi32 – 35Combined sources4
Helixi44 – 49Combined sources6
Beta strandi50 – 52Combined sources3
Beta strandi57 – 63Combined sources7
Turni64 – 66Combined sources3
Beta strandi67 – 69Combined sources3
Beta strandi75 – 80Combined sources6
Helixi81 – 84Combined sources4
Beta strandi95 – 100Combined sources6
Beta strandi103 – 112Combined sources10
Beta strandi114 – 121Combined sources8
Beta strandi129 – 141Combined sources13
Helixi145 – 149Combined sources5
Beta strandi158 – 160Combined sources3
Beta strandi177 – 182Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2K8INMR-A1-165[»]
2KFWNMR-A1-196[»]
ProteinModelPortaliP0A9K9.
SMRiP0A9K9.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A9K9.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 95PPIase FKBP-typePROSITE-ProRule annotationAdd BLAST95

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 69PPIase first partAdd BLAST69
Regioni76 – 120IF-chaperoneAdd BLAST45
Regioni129 – 151PPIase second partAdd BLAST23
Regioni152 – 196Metal-bindingAdd BLAST45

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi141 – 146Glu-rich (acidic)6
Compositional biasi148 – 179His-rich (basic)Add BLAST32
Compositional biasi166 – 194Gly-richAdd BLAST29

Domaini

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 similaritiesi

Belongs to the FKBP-type PPIase family.Curated
Contains 1 PPIase FKBP-type domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4108YZY. Bacteria.
COG1047. LUCA.
HOGENOMiHOG000154889.
InParanoidiP0A9K9.
KOiK03775.
OMAiPKDVFVG.
PhylomeDBiP0A9K9.

Family and domain databases

InterProiIPR023566. PPIase_FKBP.
IPR001179. PPIase_FKBP_dom.
[Graphical view]
PANTHERiPTHR10516. PTHR10516. 2 hits.
PfamiPF00254. FKBP_C. 1 hit.
[Graphical view]
PROSITEiPS50059. FKBP_PPIASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0A9K9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKVAKDLVVS LAYQVRTEDG VLVDESPVSA PLDYLHGHGS LISGLETALE
60 70 80 90 100
GHEVGDKFDV AVGANDAYGQ YDENLVQRVP KDVFMGVDEL QVGMRFLAET
110 120 130 140 150
DQGPVPVEIT AVEDDHVVVD GNHMLAGQNL KFNVEVVAIR EATEEELAHG
160 170 180 190
HVHGAHDHHH DHDHDGCCGG HGHDHGHEHG GEGCCGGKGN GGCGCH
Length:196
Mass (Da):20,853
Last modified:July 19, 2005 - v1
Checksum:i46DCC7C7ECD61DBA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z21496 Genomic DNA. Translation: CAA79705.1.
L13261 Unassigned DNA. Translation: AAA18574.1.
L28082 Genomic DNA. Translation: AAC41458.1.
U18997 Genomic DNA. Translation: AAA58146.1.
U00096 Genomic DNA. Translation: AAC76374.1.
AP009048 Genomic DNA. Translation: BAE77942.1.
PIRiA49987.
RefSeqiNP_417808.1. NC_000913.3.
WP_000861334.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76374; AAC76374; b3349.
BAE77942; BAE77942; BAE77942.
GeneIDi947859.
KEGGiecj:JW3311.
eco:b3349.
PATRICi32122130. VBIEscCol129921_3442.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z21496 Genomic DNA. Translation: CAA79705.1.
L13261 Unassigned DNA. Translation: AAA18574.1.
L28082 Genomic DNA. Translation: AAC41458.1.
U18997 Genomic DNA. Translation: AAA58146.1.
U00096 Genomic DNA. Translation: AAC76374.1.
AP009048 Genomic DNA. Translation: BAE77942.1.
PIRiA49987.
RefSeqiNP_417808.1. NC_000913.3.
WP_000861334.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2K8INMR-A1-165[»]
2KFWNMR-A1-196[»]
ProteinModelPortaliP0A9K9.
SMRiP0A9K9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260682. 10 interactors.
DIPiDIP-31853N.
IntActiP0A9K9. 119 interactors.
MINTiMINT-1223693.
STRINGi511145.b3349.

Proteomic databases

EPDiP0A9K9.
PaxDbiP0A9K9.
PRIDEiP0A9K9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76374; AAC76374; b3349.
BAE77942; BAE77942; BAE77942.
GeneIDi947859.
KEGGiecj:JW3311.
eco:b3349.
PATRICi32122130. VBIEscCol129921_3442.

Organism-specific databases

EchoBASEiEB1614.
EcoGeneiEG11663. slyD.

Phylogenomic databases

eggNOGiENOG4108YZY. Bacteria.
COG1047. LUCA.
HOGENOMiHOG000154889.
InParanoidiP0A9K9.
KOiK03775.
OMAiPKDVFVG.
PhylomeDBiP0A9K9.

Enzyme and pathway databases

BioCyciEcoCyc:EG11663-MONOMER.
ECOL316407:JW3311-MONOMER.
MetaCyc:EG11663-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0A9K9.
PROiP0A9K9.

Family and domain databases

InterProiIPR023566. PPIase_FKBP.
IPR001179. PPIase_FKBP_dom.
[Graphical view]
PANTHERiPTHR10516. PTHR10516. 2 hits.
PfamiPF00254. FKBP_C. 1 hit.
[Graphical view]
PROSITEiPS50059. FKBP_PPIASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSLYD_ECOLI
AccessioniPrimary (citable) accession number: P0A9K9
Secondary accession number(s): P30856, Q2M714
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2005
Last sequence update: July 19, 2005
Last modified: November 2, 2016
This is version 100 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.