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P0A9K9

- SLYD_ECOLI

UniProt

P0A9K9 - SLYD_ECOLI

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Protein

FKBP-type peptidyl-prolyl cis-trans isomerase SlyD

Gene
slyD, b3349, JW3311
Organism
Escherichia coli (strain K12)
Status
Reviewed - 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.6 Publications
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.6 Publications
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.6 Publications

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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi167 – 1671Nickel Reviewed prediction
Metal bindingi168 – 1681Nickel Reviewed prediction
Metal bindingi184 – 1841Nickel Reviewed prediction
Metal bindingi185 – 1851Nickel Reviewed prediction
Metal bindingi193 – 1931Nickel Reviewed prediction
Metal bindingi195 – 1951Nickel Reviewed prediction

GO - Molecular functioni

  1. cobalt ion binding Source: EcoCyc
  2. copper ion binding Source: EcoCyc
  3. FK506 binding Source: RefGenome
  4. nickel cation binding Source: EcoCyc
  5. peptidyl-prolyl cis-trans isomerase activity Source: EcoCyc
  6. protein binding Source: IntAct
  7. unfolded protein binding Source: EcoCyc
  8. zinc ion binding Source: EcoCyc

GO - Biological processi

  1. chaperone-mediated protein folding Source: RefGenome
  2. protein maturation Source: EcoCyc
  3. protein maturation by protein folding Source: EcoliWiki
  4. protein peptidyl-prolyl isomerization Source: GOC
  5. protein refolding Source: EcoCyc
  6. protein stabilization Source: EcoliWiki
  7. 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG11663. slyD.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: RefGenome
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi42 – 421I → 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. 2 Publications
Mutagenesisi132 – 1321F → Y: Almost complete loss of PPIase activity, but has little impact on chaperone activity and interaction with HypB; when associated with S-42. 2 Publications
Mutagenesisi167 – 1682CC → AA: Reduces nickel-binding capacity. 1 Publication
Mutagenesisi184 – 1852CC → AA: Reduces nickel-binding capacity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 196196FKBP-type peptidyl-prolyl cis-trans isomerase SlyDPRO_0000075355Add
BLAST

Proteomic databases

PaxDbiP0A9K9.
PRIDEiP0A9K9.

Expressioni

Gene expression databases

GenevestigatoriP0A9K9.

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

Protein-protein interaction databases

DIPiDIP-31853N.
IntActiP0A9K9. 119 interactions.
MINTiMINT-1223693.
STRINGi511145.b3349.

Structurei

Secondary structure

1
196
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi7 – 1711
Turni18 – 203
Beta strandi22 – 254
Beta strandi28 – 303
Beta strandi32 – 354
Helixi44 – 496
Beta strandi50 – 523
Beta strandi57 – 637
Turni64 – 663
Beta strandi67 – 693
Beta strandi75 – 806
Helixi81 – 844
Beta strandi95 – 1006
Beta strandi103 – 11210
Beta strandi114 – 1218
Beta strandi129 – 14113
Helixi145 – 1495
Beta strandi158 – 1603
Beta strandi177 – 1826

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2K8INMR-A1-165[»]
2KFWNMR-A1-196[»]
ProteinModelPortaliP0A9K9.
SMRiP0A9K9. Positions 1-148.

Miscellaneous databases

EvolutionaryTraceiP0A9K9.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 9595PPIase FKBP-typeAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 6969PPIase first partAdd
BLAST
Regioni76 – 12045IF-chaperoneAdd
BLAST
Regioni129 – 15123PPIase second partAdd
BLAST
Regioni152 – 19645Metal-bindingAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi141 – 1466Glu-rich (acidic)
Compositional biasi148 – 17932His-rich (basic)Add
BLAST
Compositional biasi166 – 19429Gly-richAdd
BLAST

Domaini

The N-terminal region consists of two globular folded domains that contain prolyl isomerase and chaperone activities.5 Publications
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.5 Publications

Sequence similaritiesi

Belongs to the FKBP-type PPIase family.

Phylogenomic databases

eggNOGiCOG1047.
HOGENOMiHOG000154889.
KOiK03775.
OMAiHMLAGQT.
OrthoDBiEOG6Q8J79.
PhylomeDBiP0A9K9.

Family and domain databases

InterProiIPR023566. PPIase_FKBP.
IPR001179. PPIase_FKBP_dom.
[Graphical view]
PANTHERiPTHR10516. PTHR10516. 1 hit.
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

MKVAKDLVVS LAYQVRTEDG VLVDESPVSA PLDYLHGHGS LISGLETALE    50
GHEVGDKFDV AVGANDAYGQ YDENLVQRVP KDVFMGVDEL QVGMRFLAET 100
DQGPVPVEIT AVEDDHVVVD GNHMLAGQNL KFNVEVVAIR EATEEELAHG 150
HVHGAHDHHH DHDHDGCCGG HGHDHGHEHG GEGCCGGKGN GGCGCH 196
Length:196
Mass (Da):20,853
Last modified:July 19, 2005 - v1
Checksum:i46DCC7C7ECD61DBA
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.
YP_492083.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC76374; AAC76374; b3349.
BAE77942; BAE77942; BAE77942.
GeneIDi12931688.
947859.
KEGGiecj:Y75_p3827.
eco:b3349.
PATRICi32122130. VBIEscCol129921_3442.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
PIRi A49987.
RefSeqi NP_417808.1. NC_000913.3.
YP_492083.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2K8I NMR - A 1-165 [» ]
2KFW NMR - A 1-196 [» ]
ProteinModelPortali P0A9K9.
SMRi P0A9K9. Positions 1-148.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-31853N.
IntActi P0A9K9. 119 interactions.
MINTi MINT-1223693.
STRINGi 511145.b3349.

Proteomic databases

PaxDbi P0A9K9.
PRIDEi P0A9K9.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC76374 ; AAC76374 ; b3349 .
BAE77942 ; BAE77942 ; BAE77942 .
GeneIDi 12931688.
947859.
KEGGi ecj:Y75_p3827.
eco:b3349.
PATRICi 32122130. VBIEscCol129921_3442.

Organism-specific databases

EchoBASEi EB1614.
EcoGenei EG11663. slyD.

Phylogenomic databases

eggNOGi COG1047.
HOGENOMi HOG000154889.
KOi K03775.
OMAi HMLAGQT.
OrthoDBi EOG6Q8J79.
PhylomeDBi P0A9K9.

Enzyme and pathway databases

BioCyci EcoCyc:EG11663-MONOMER.
ECOL316407:JW3311-MONOMER.
MetaCyc:EG11663-MONOMER.

Miscellaneous databases

EvolutionaryTracei P0A9K9.
PROi P0A9K9.

Gene expression databases

Genevestigatori P0A9K9.

Family and domain databases

InterProi IPR023566. PPIase_FKBP.
IPR001179. PPIase_FKBP_dom.
[Graphical view ]
PANTHERi PTHR10516. PTHR10516. 1 hit.
Pfami PF00254. FKBP_C. 1 hit.
[Graphical view ]
PROSITEi PS50059. FKBP_PPIASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "An Escherichia coli protein consisting of a domain homologous to FK506-binding proteins (FKBP) and a new metal binding motif."
    Wuelfing C., Lomardero J., Plueckthun A.
    J. Biol. Chem. 269:2895-2901(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-35 AND 141-146.
    Strain: K12 / ATCC 35607 / JM83.
  2. "slyD, a host gene required for phi X174 lysis, is related to the FK506-binding protein family of peptidyl-prolyl cis-trans-isomerases."
    Roof W.D., Horne S.M., Young K.D., Young R.
    J. Biol. Chem. 269:2902-2910(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12 / CS109.
  3. "Escherichia coli and other species of the Enterobacteriaceae encode a protein similar to the family of Mip-like FK506-binding proteins."
    Horne S.M., Young K.D.
    Arch. Microbiol. 163:357-365(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12 / CS109.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "The Escherichia coli SlyD is a metal ion-regulated peptidyl-prolyl cis/trans-isomerase."
    Hottenrott S., Schumann T., Plueckthun A., Fischer G., Rahfeld J.-U.
    J. Biol. Chem. 272:15697-15701(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-10, ENZYME REGULATION, CHARACTERIZATION.
    Strain: BL21.
  7. "The Escherichia coli FKBP-type PPIase SlyD is required for the stabilization of the E lysis protein of bacteriophage phi X174."
    Bernhardt T.G., Roof W.D., Young R.
    Mol. Microbiol. 45:99-108(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN LYSIS OF PHIX174 INFECTED CELLS.
  8. "A role for SlyD in the Escherichia coli hydrogenase biosynthetic pathway."
    Zhang J.W., Butland G., Greenblatt J.F., Emili A., Zamble D.B.
    J. Biol. Chem. 280:4360-4366(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN HYDROGENASE METALLOCENTER ASSEMBLY, INTERACTION WITH HYPB.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  9. "SlyD proteins from different species exhibit high prolyl isomerase and chaperone activities."
    Scholz C., Eckert B., Hagn F., Schaarschmidt P., Balbach J., Schmid F.X.
    Biochemistry 45:20-33(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A CHAPERONE AND A PPIASE, CATALYTIC ACTIVITY, ENZYME REGULATION, DOMAIN.
  10. "The peptidyl-prolyl isomerase activity of SlyD is not required for maturation of Escherichia coli hydrogenase."
    Zhang J.W., Leach M.R., Zamble D.B.
    J. Bacteriol. 189:7942-7944(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN HYDROGENASE METALLOCENTER ASSEMBLY, DOMAIN, MUTAGENESIS OF ILE-42 AND PHE-132.
  11. "DnaK plays a pivotal role in Tat targeting of CueO and functions beside SlyD as a general Tat signal binding chaperone."
    Graubner W., Schierhorn A., Bruser T.
    J. Biol. Chem. 282:7116-7124(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH TAT SIGNAL SEQUENCES.
    Strain: K12 / MC4100 / JA176.
  12. Cited for: SUBUNIT, NICKEL-BINDING, DOMAIN, MUTAGENESIS OF 167-CYS-CYS-168 AND 184-CYS-CYS-185.
  13. "The interaction of the Escherichia coli protein SlyD with nickel ions illuminates the mechanism of regulation of its peptidyl-prolyl isomerase activity."
    Martino L., He Y., Hands-Taylor K.L., Valentine E.R., Kelly G., Giancola C., Conte M.R.
    FEBS J. 276:4529-4544(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR, NICKEL-BINDING, DOMAIN.
  14. "NMR solution structure of SlyD from Escherichia coli: spatial separation of prolyl isomerase and chaperone function."
    Weininger U., Haupt C., Schweimer K., Graubner W., Kovermann M., Bruser T., Scholz C., Schaarschmidt P., Zoldak G., Schmid F.X., Balbach J.
    J. Mol. Biol. 387:295-305(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 1-165, FUNCTION AS A CHAPERONE, DOMAIN, BINDING TO UNFOLDED PROTEINS.

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: September 3, 2014
This is version 82 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

External Data

Dasty 3

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