slyD:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

SlyD

Synonyms

FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)[1], B3349[2][1], SlyD[2][1], WHP[2][1] , ECK3336, JW3311, b3349

Product description

FKBP-type rotamase, peptidyl prolyl cis-trans isomerase[2]; FKBP-type peptidyl prolyl cis-trans isomerase[3];

Component of FKBP-type peptidyl prolyl cis-trans isomerase[3]

FKBP-type peptidyl-prolyl cis-trans isomerase; metal ion regulated; overexpression causes filamentation; required to stabilize E lysis protein of bacteriophage phiX174[4]

EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0003755

peptidyl-prolyl cis-trans isomerase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:5.2.1.8

F

Seeded from EcoCyc (v14.0)

complete

GO:0003755

peptidyl-prolyl cis-trans isomerase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0697

F

Seeded from EcoCyc (v14.0)

complete

GO:0005507

copper ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0186

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

PMID:8300624[5]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016151

nickel ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0533

F

Seeded from EcoCyc (v14.0)

complete

GO:0016151

nickel ion binding

PMID:19947632[6]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016151

nickel ion binding

PMID:8300624[5]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0050897

cobalt ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0170

F

Seeded from EcoCyc (v14.0)

complete

GO:0051082

unfolded protein binding

PMID:19356587[7]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

PMID:15569666[8]

IPI: Inferred from Physical Interaction

UniProtKB:P0AAN3

F

complete

GO:0051604

protein maturation

PMID:17426034[9]

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc (v14.0)

complete

GO:0022417

protein maturation by protein folding

PMID:15569666[8]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0016151

nickel ion binding

PMID:19645725[10]

IDA: Inferred from Direct Assay

F

complete

GO:0009408

response to heat

PMID:17971396[11]

IEP: Inferred from Expression Pattern

P

complete

GO:0050821

protein stabilization

PMID:17971396[11]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0003755

peptidyl-prolyl cis-trans isomerase activity

PMID:17720786[12]

IMP: Inferred from Mutant Phenotype

F

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

Subunits of FKBP-type peptidyl prolyl cis-trans isomerase

could be indirect

Protein

gltL

PMID:15690043[13]

Experiment(s):EBI-893588

Protein

hupA

PMID:15690043[13]

Experiment(s):EBI-893588

Protein

hupB

PMID:15690043[13]

Experiment(s):EBI-893588

Protein

hypB

PMID:15690043[13]

Experiment(s):EBI-893588

Protein

sapD

PMID:15690043[13]

Experiment(s):EBI-893588

Protein

serS

PMID:15690043[13]

Experiment(s):EBI-893588

Protein

ulaF

PMID:15690043[13]

Experiment(s):EBI-893588

Protein

ydeI

PMID:15690043[13]

Experiment(s):EBI-893588

Protein

nudL

PMID:15690043[13]

Experiment(s):EBI-893588

Protein

grcA

PMID:15690043[13]

Experiment(s):EBI-893588

Protein

yhjQ

PMID:15690043[13]

Experiment(s):EBI-893588

Protein

ycgX

PMID:16606699[14]

Experiment(s):EBI-1145639

Protein

rplE

PMID:16606699[14]

Experiment(s):EBI-1145639

Protein

insA7

PMID:16606699[14]

Experiment(s):EBI-1145639

Protein

betA

PMID:16606699[14]

Experiment(s):EBI-1145639

Protein

rpmA

PMID:16606699[14]

Experiment(s):EBI-1145639

Protein

rplW

PMID:16606699[14]

Experiment(s):EBI-1145639

Protein

rplO

PMID:16606699[14]

Experiment(s):EBI-1145639

Protein

rplF

PMID:16606699[14]

Experiment(s):EBI-1145639

Protein

fliC

PMID:16606699[14]

Experiment(s):EBI-1145639

Protein

rplN

PMID:16606699[14]

Experiment(s):EBI-1145639

Protein

rpsI

PMID:16606699[14]

Experiment(s):EBI-1145639

Protein

lacI

PMID:16606699[14]

Experiment(s):EBI-1145639

Protein

rpsD

PMID:16606699[14]

Experiment(s):EBI-1145639

Protein

yhdZ

PMID:16606699[14]

Experiment(s):EBI-1145639

Protein

rpsE

PMID:16606699[14]

Experiment(s):EBI-1145639

Protein

nusG

PMID:16606699[14]

Experiment(s):EBI-1145639

Protein

yfiD

PMID:19402753[15]

LCMS(ID Probability):99.0 MALDI(Z-score):3.263244

Protein

ampH

PMID:19402753[15]

LCMS(ID Probability):99.6

Protein

HypB (GTPase & hydrogenase accessory protein)

HypB was shown to directly interact with SlyD & a slyD- strain has reduced hydrogenase activity & accumulates an immature (unprocessed) form of the hydrogenase (HycE), which can be complemented by the addition of nickel to the growth medium or complemented with plasmid-borne expression of SlyD. See PMID:15569666[8]


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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MKVAKDLVVS LAYQVRTEDG VLVDESPVSA PLDYLHGHGS LISGLETALE GHEVGDKFDV
AVGANDAYGQ YDENLVQRVP KDVFMGVDEL QVGMRFLAET DQGPVPVEIT AVEDDHVVVD
GNHMLAGQNL KFNVEVVAIR EATEEELAHG HVHGAHDHHH DHDHDGCCGG HGHDHGHEHG
GEGCCGGKGN GGCGCH
Length

196

Mol. Wt

20.85 kDa

pI

4.8 (calculated)

Extinction coefficient

5,960 - 6,710 (calc based on 4 Y, 0 W, and 6 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

1..137

PF00254 FKBP-type peptidyl-prolyl cis-trans isomerase

PMID:19920124[16]

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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=slyD taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16131228

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947859

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010946

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A9K9

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11663

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11663

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947859

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001606

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1614

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 Wülfing, C et al. (1994) An Escherichia coli protein consisting of a domain homologous to FK506-binding proteins (FKBP) and a new metal binding motif. J. Biol. Chem. 269 2895-901 PubMed
  6. ↑ Kaluarachchi, H et al. (2009) The Ni(II)-binding properties of the metallochaperone SlyD. J. Am. Chem. Soc. 131 18489-500 PubMed
  7. ↑ Weininger, U et al. (2009) NMR solution structure of SlyD from Escherichia coli: spatial separation of prolyl isomerase and chaperone function. J. Mol. Biol. 387 295-305 PubMed
  8. ↑ 8.0 8.1 8.2 Zhang, JW et al. (2005) A role for SlyD in the Escherichia coli hydrogenase biosynthetic pathway. J. Biol. Chem. 280 4360-6 PubMed
  9. ↑ Leach, MR et al. (2007) The role of complex formation between the Escherichia coli hydrogenase accessory factors HypB and SlyD. J. Biol. Chem. 282 16177-86 PubMed
  10. ↑ Martino, L et al. (2009) The interaction of the Escherichia coli protein SlyD with nickel ions illuminates the mechanism of regulation of its peptidyl-prolyl isomerase activity. FEBS J. 276 4529-44 PubMed
  11. ↑ 11.0 11.1 Han, KY et al. (2007) Solubilization of aggregation-prone heterologous proteins by covalent fusion of stress-responsive Escherichia coli protein, SlyD. Protein Eng. Des. Sel. 20 543-9 PubMed
  12. ↑ Zhang, JW et al. (2007) The peptidyl-prolyl isomerase activity of SlyD is not required for maturation of Escherichia coli hydrogenase. J. Bacteriol. 189 7942-4 PubMed
  13. ↑ 13.00 13.01 13.02 13.03 13.04 13.05 13.06 13.07 13.08 13.09 13.10 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  14. ↑ 14.00 14.01 14.02 14.03 14.04 14.05 14.06 14.07 14.08 14.09 14.10 14.11 14.12 14.13 14.14 14.15 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  15. ↑ 15.0 15.1 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  16. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

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