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P0A9K9

- SLYD_ECOLI

UniProt

P0A9K9 - SLYD_ECOLI

Protein

FKBP-type peptidyl-prolyl cis-trans isomerase SlyD

Gene

slyD

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 83 (01 Oct 2014)
      Sequence version 1 (19 Jul 2005)
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    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)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi167 – 1671NickelSequence Analysis
    Metal bindingi168 – 1681NickelSequence Analysis
    Metal bindingi184 – 1841NickelSequence Analysis
    Metal bindingi185 – 1851NickelSequence Analysis
    Metal bindingi193 – 1931NickelSequence Analysis
    Metal bindingi195 – 1951NickelSequence Analysis

    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

    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

    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A9K9.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 9595PPIase FKBP-typePROSITE-ProRule annotationAdd
    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.
    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

    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

    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: October 1, 2014
    This is version 83 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