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P0A9K9 (SLYD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 81. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
FKBP-type peptidyl-prolyl cis-trans isomerase SlyD

Short name=PPIase
EC=5.2.1.8
Alternative name(s):
Histidine-rich protein
Metallochaperone SlyD
Rotamase
Sensitivity to lysis protein D
WHP
Gene names
Name:slyD
Ordered Locus Names:b3349, JW3311
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length196 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.14

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. Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.14

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. Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.14

Catalytic activity

Peptidylproline (omega=180) = peptidylproline (omega=0). Ref.9

Enzyme 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. Ref.6 Ref.9

Subunit structure

Monomer. Binds to a broad range of unrelated Tat signal sequences. Interacts with the hydrogenase nickel incorporation protein HypB. Ref.8 Ref.11 Ref.12

Subcellular location

Cytoplasm.

Domain

The N-terminal region consists of two globular folded domains that contain prolyl isomerase and chaperone activities. Ref.9 Ref.10 Ref.12 Ref.13 Ref.14

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. Ref.9 Ref.10 Ref.12 Ref.13 Ref.14

Miscellaneous

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

Sequence similarities

Belongs to the FKBP-type PPIase family.

Contains 1 PPIase FKBP-type domain.

Ontologies

Keywords
   Cellular componentCytoplasm
   LigandCobalt
Copper
Metal-binding
Nickel
Zinc
   Molecular functionChaperone
Isomerase
Rotamase
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processprotein maturation

Inferred from mutant phenotype PubMed 17426034. Source: EcoCyc

protein maturation by protein folding

Inferred from mutant phenotype Ref.8. Source: EcoliWiki

protein peptidyl-prolyl isomerization

Inferred from direct assay Ref.6. Source: GOC

protein refolding

Inferred from direct assay Ref.9. Source: EcoCyc

protein stabilization

Inferred from mutant phenotype PubMed 17971396. Source: EcoliWiki

response to heat

Inferred from expression pattern PubMed 17971396. Source: EcoliWiki

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

membrane

Inferred from Biological aspect of Ancestor. Source: RefGenome

   Molecular_functionFK506 binding

Inferred from Biological aspect of Ancestor. Source: RefGenome

cobalt ion binding

Inferred from direct assay PubMed 22047179. Source: EcoCyc

copper ion binding

Inferred from direct assay PubMed 22047179. Source: EcoCyc

nickel cation binding

Inferred from direct assay Ref.13Ref.12PubMed 22047179Ref.1. Source: EcoCyc

peptidyl-prolyl cis-trans isomerase activity

Inferred from direct assay Ref.6. Source: EcoCyc

protein binding

Inferred from physical interaction PubMed 15690043PubMed 16412426PubMed 21185288PubMed 22016389. Source: IntAct

unfolded protein binding

Inferred from direct assay Ref.14. Source: EcoCyc

zinc ion binding

Inferred from direct assay PubMed 22047179Ref.1. Source: EcoCyc

Complete GO annotation...

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 196196FKBP-type peptidyl-prolyl cis-trans isomerase SlyD
PRO_0000075355

Regions

Domain1 – 9595PPIase FKBP-type
Region1 – 6969PPIase first part
Region76 – 12045IF-chaperone
Region129 – 15123PPIase second part
Region152 – 19645Metal-binding
Compositional bias141 – 1466Glu-rich (acidic)
Compositional bias148 – 17932His-rich (basic)
Compositional bias166 – 19429Gly-rich

Sites

Metal binding1671Nickel Potential
Metal binding1681Nickel Potential
Metal binding1841Nickel Potential
Metal binding1851Nickel Potential
Metal binding1931Nickel Potential
Metal binding1951Nickel Potential

Experimental info

Mutagenesis421I → 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. Ref.10 Ref.12
Mutagenesis1321F → Y: Almost complete loss of PPIase activity, but has little impact on chaperone activity and interaction with HypB; when associated with S-42. Ref.10 Ref.12
Mutagenesis167 – 1682CC → AA: Reduces nickel-binding capacity. Ref.12
Mutagenesis184 – 1852CC → AA: Reduces nickel-binding capacity. Ref.12

Secondary structure

.................................. 196
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0A9K9 [UniParc].

Last modified July 19, 2005. Version 1.
Checksum: 46DCC7C7ECD61DBA

FASTA19620,853
        10         20         30         40         50         60 
MKVAKDLVVS LAYQVRTEDG VLVDESPVSA PLDYLHGHGS LISGLETALE GHEVGDKFDV 

        70         80         90        100        110        120 
AVGANDAYGQ YDENLVQRVP KDVFMGVDEL QVGMRFLAET DQGPVPVEIT AVEDDHVVVD 

       130        140        150        160        170        180 
GNHMLAGQNL KFNVEVVAIR EATEEELAHG HVHGAHDHHH DHDHDGCCGG HGHDHGHEHG 

       190 
GEGCCGGKGN GGCGCH 

« Hide

References

« Hide 'large scale' references
[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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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]"The Ni(II)-binding properties of the metallochaperone SlyD."
Kaluarachchi H., Sutherland D.E., Young A., Pickering I.J., Stillman M.J., Zamble D.B.
J. Am. Chem. Soc. 131:18489-18500(2009) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRA49987.
RefSeqNP_417808.1. NC_000913.3.
YP_492083.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2K8INMR-A1-165[»]
2KFWNMR-A1-196[»]
ProteinModelPortalP0A9K9.
SMRP0A9K9. Positions 1-148.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-31853N.
IntActP0A9K9. 119 interactions.
MINTMINT-1223693.
STRING511145.b3349.

Proteomic databases

PaxDbP0A9K9.
PRIDEP0A9K9.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76374; AAC76374; b3349.
BAE77942; BAE77942; BAE77942.
GeneID12931688.
947859.
KEGGecj:Y75_p3827.
eco:b3349.
PATRIC32122130. VBIEscCol129921_3442.

Organism-specific databases

EchoBASEEB1614.
EcoGeneEG11663. slyD.

Phylogenomic databases

eggNOGCOG1047.
HOGENOMHOG000154889.
KOK03775.
OMAHMLAGQT.
OrthoDBEOG6Q8J79.
PhylomeDBP0A9K9.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorP0A9K9.

Family and domain databases

InterProIPR023566. PPIase_FKBP.
IPR001179. PPIase_FKBP_dom.
[Graphical view]
PANTHERPTHR10516. PTHR10516. 1 hit.
PfamPF00254. FKBP_C. 1 hit.
[Graphical view]
PROSITEPS50059. FKBP_PPIASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP0A9K9.
PROP0A9K9.

Entry information

Entry nameSLYD_ECOLI
AccessionPrimary (citable) accession number: P0A9K9
Secondary accession number(s): P30856, Q2M714
Entry history
Integrated into UniProtKB/Swiss-Prot: July 19, 2005
Last sequence update: July 19, 2005
Last modified: July 9, 2014
This is version 81 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene