slyD:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

slyD

Gene Synonym(s)

ECK3336, b3349, JW3311[1], JW3311

Product Desc.

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]

Product Synonyms(s)

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

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): slyD[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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HypB requires binding of SlyD for hydrogenase activity as SlyD helps facilitate nickel insertion. Binds TrxA (Kumar, 2004). SlyD has a histidine-rich, nickel-binding region, so it is a common contaminant in protein purification of His-tagged proteins (Parsy, 2007). SlyD is a a heat-shock protein that facilitates folding and enhances the solubilty of aggregation-prone proteins (Han, 2007).[4]



Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

slyD

Mnemonic

Sensitivity to lysis

Synonyms

ECK3336, b3349, JW3311[1], JW3311

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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

74.92 minutes, 74.92 minutes 

MG1655: 3476519..3475929
<gbrowseImage> name=NC_000913:3475929..3476519 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3406402..3405812
<gbrowseImage> name=NC_012967:3405812..3406402 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3363086..3363676
<gbrowseImage> name=NC_012759:3363086..3363676 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4161919..4162509
<gbrowseImage> name=NC_007779:4161919..4162509 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3574264..3573674
<gbrowseImage> name=NC_010473:3573674..3574264 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

3475929

Edman degradation

PMID:8300624
PMID:9188461


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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔslyD (Keio:JW3311)

deletion

deletion

PMID:16738554

Shigen
CGSC8289[5]

ΔslyD738::kan

PMID:16738554

CGSC:93041


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW3311

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAAGTAGCAAAAGACCTGGT

Primer 2:CCGTGGCAACCGCAACCGCCGTT

4C5

Kohara Phage

Genobase

PMID:3038334

3F8

Kohara Phage

Genobase

PMID:3038334

smg-3082::Tn10

Linked marker

CAG12071 = CGSC7444[5]

est. P1 cotransduction: 12% [6]
Synonyms:zhb-3082::Tn10, zhd-3082::Tn10

zhf-3084::Tn10

Linked marker

CAG18456 = CGSC7576[5]

est. P1 cotransduction: 36% [6]
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).

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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

EcoCyc

EcoCyc:EG11663

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11663

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001606

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947859

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1614

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010946

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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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

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

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016151

nickel ion binding

PMID:8300624

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

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

PMID:15569666

IPI: Inferred from Physical Interaction

UniProtKB:P0AAN3

F

complete

GO:0051604

protein maturation

PMID:17426034

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc (v14.0)

complete

GO:0022417

protein maturation by protein folding

PMID:15569666

IMP: Inferred from Mutant Phenotype

P

complete

GO:0016151

nickel ion binding

PMID:19645725

IDA: Inferred from Direct Assay

F

complete

GO:0009408

response to heat

PMID:17971396

IEP: Inferred from Expression Pattern

P

complete

GO:0050821

protein stabilization

PMID:17971396

IMP: Inferred from Mutant Phenotype

P

complete

GO:0003755

peptidyl-prolyl cis-trans isomerase activity

PMID:17720786

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

Experiment(s):EBI-893588

Protein

hupA

PMID:15690043

Experiment(s):EBI-893588

Protein

hupB

PMID:15690043

Experiment(s):EBI-893588

Protein

hypB

PMID:15690043

Experiment(s):EBI-893588

Protein

sapD

PMID:15690043

Experiment(s):EBI-893588

Protein

serS

PMID:15690043

Experiment(s):EBI-893588

Protein

ulaF

PMID:15690043

Experiment(s):EBI-893588

Protein

ydeI

PMID:15690043

Experiment(s):EBI-893588

Protein

nudL

PMID:15690043

Experiment(s):EBI-893588

Protein

grcA

PMID:15690043

Experiment(s):EBI-893588

Protein

yhjQ

PMID:15690043

Experiment(s):EBI-893588

Protein

ycgX

PMID:16606699

Experiment(s):EBI-1145639

Protein

rplE

PMID:16606699

Experiment(s):EBI-1145639

Protein

insA7

PMID:16606699

Experiment(s):EBI-1145639

Protein

betA

PMID:16606699

Experiment(s):EBI-1145639

Protein

rpmA

PMID:16606699

Experiment(s):EBI-1145639

Protein

rplW

PMID:16606699

Experiment(s):EBI-1145639

Protein

rplO

PMID:16606699

Experiment(s):EBI-1145639

Protein

rplF

PMID:16606699

Experiment(s):EBI-1145639

Protein

fliC

PMID:16606699

Experiment(s):EBI-1145639

Protein

rplN

PMID:16606699

Experiment(s):EBI-1145639

Protein

rpsI

PMID:16606699

Experiment(s):EBI-1145639

Protein

lacI

PMID:16606699

Experiment(s):EBI-1145639

Protein

rpsD

PMID:16606699

Experiment(s):EBI-1145639

Protein

yhdZ

PMID:16606699

Experiment(s):EBI-1145639

Protein

rpsE

PMID:16606699

Experiment(s):EBI-1145639

Protein

nusG

PMID:16606699

Experiment(s):EBI-1145639

Protein

yfiD

PMID:19402753

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

Protein

ampH

PMID:19402753

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


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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

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<motif_map/>

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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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

5.85E+03

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

Ecoli K-12

482.605+/-4.428

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.23487+/-0.01604

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by FISH

PMID:20671182

mRNA

Ecoli K-12

1.038135593

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

38169

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

7302

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

20452

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

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

Transcription unit(s)

slyD

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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:3476499..3476539 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b3349 (EcoliWiki Page)

NCBI GEO profiles for slyD

microarray

GenExpDB:b3349 (EcoliWiki Page)

Summary of data for slyD from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (3476053..3476465) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ09; Well:B2[7]

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Notes

Accessions Related to slyD Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11663

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1614

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3349

EcoGene

EcoGene:EG11663

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001606

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010946

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Evolution

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Homologs in Other Organisms

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

Organism Homologs (Statistics) Comments

Xenopus tropicalis

  • ENSXETP00000041168 (score: 1.000; bootstrap: 73%)

From Inparanoid:20070104

Shigella flexneri

SLYD

From SHIGELLACYC

E. coli O157

SLYD

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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

Database Accession Notes

Pfam (EcoliWiki Page)

PF00254 FKBP-type peptidyl-prolyl cis-trans isomerase

Superfamily (EcoliWiki Page)

SUPERFAMILY:54534

EcoCyc

EcoCyc:EG11663

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11663

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

ASAP

ASAP:ABE-0010946

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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 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 2.4 2.5 2.6 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 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 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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