RegulonDB RegulonDB 10.9: Gene Form
   

slyD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

slyD slyX yheV anti-anti-terminator anti-terminator terminator slyDp6 slyDp6 TSS_3952 TSS_3952 slyDp5 slyDp5 slyDp7 slyDp7 TSS_3951 TSS_3951

Gene      
Name: slyD    Texpresso search in the literature
Synonym(s): ECK3336, EG11663, b3349
Genome position(nucleotides): 3477907 <-- 3478497 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
55.33
External database links:  
ASAP:
ABE-0010946
CGSC:
35441
ECHOBASE:
EB1614
ECOLIHUB:
slyD
OU-MICROARRAY:
b3349
STRING:
511145.b3349
COLOMBOS: slyD


Product      
Name: FKBP-type peptidyl-prolyl cis-trans isomerase SlyD
Synonym(s): SlyD, WHP
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 20.853
Isoelectric point: 4.685
Motif(s):
 
Type Positions Sequence
42 -> 42 I
148 -> 179 AHGHVHGAHDHHHDHDHDGCCGGHGHDHGHEH
1 -> 95 MKVAKDLVVSLAYQVRTEDGVLVDESPVSAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENLVQRVPKDVFMGVDELQVGMR
132 -> 132 F
129 -> 151 NLKFNVEVVAIREATEEELAHGH

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.4 - chaperoning, repair (refolding)
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0005507 - copper ion binding
GO:0005515 - protein binding
GO:0016853 - isomerase activity
GO:0046872 - metal ion binding
GO:0051082 - unfolded protein binding
GO:0003755 - peptidyl-prolyl cis-trans isomerase activity
GO:0016151 - nickel cation binding
GO:0008270 - zinc ion binding
GO:0050897 - cobalt ion binding
biological_process GO:0043963 - modulation by symbiont of host adenylate cyclase-mediated signal transduction
GO:0009408 - response to heat
GO:0050821 - protein stabilization
GO:0051604 - protein maturation
GO:0042026 - protein refolding
GO:0022417 - protein maturation by protein folding
GO:0000413 - protein peptidyl-prolyl isomerization
Note(s): Note(s): ...[more].
Reference(s): [1] Bolanos-Garcia VM., et al., 2006
[2] Chen X., et al., 2017
[3] Geitner AJ., et al., 2013
[4] Haupt C., et al., 2011
[5] Hu Y., et al., 2017
[6] Kovermann M., et al., 2013
[7] Kovermann M., et al., 2011
[8] Kumar A., et al., 2017
[9] Mokhonov VV., et al., 2018
[10] Mukherjee S., et al., 2003
[11] Zamble DB. 2015
[12] Zhang F., et al., 2020
[13] Zoldak G., et al., 2013
External database links:  
DIP:
DIP-31853N
DISPROT:
DP00766
ECOCYC:
EG11663-MONOMER
ECOLIWIKI:
b3349
INTERPRO:
IPR001179
MINT:
P0A9K9
MODBASE:
P0A9K9
PDB:
2KFW
PDB:
5I7P
PDB:
2K8I
PFAM:
PF00254
PRIDE:
P0A9K9
PRODB:
PRO_000023959
PROSITE:
PS50059
REFSEQ:
NP_417808
SMR:
P0A9K9
UNIPROT:
P0A9K9


Operon      
Name: slyD         
Operon arrangement:
Transcription unit        Promoter
slyD


RNA cis-regulatory element    
Attenuation: Transcriptional


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_3951 3478525 reverse nd [RS-EPT-CBR] [14]
  promoter slyDp7 3478528 reverse Similarity to the consensus
Read more >
[ICWHO] [15]
  promoter slyDp5 3478540 reverse Similarity to the consensus
Read more >
[ICWHO] [15]
  promoter TSS_3952 3478558 reverse nd [RS-EPT-CBR] [14]
  promoter slyDp6 3478699 reverse Similarity to the consensus
Read more >
[ICWHO] [15]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Bolanos-Garcia VM., Davies OR., 2006, Structural analysis and classification of native proteins from E. coli commonly co-purified by immobilised metal affinity chromatography., Biochim Biophys Acta 1760(9):1304-13

 [2] Chen X., Nomani A., Patel N., Hatefi A., 2017, Production of low-expressing recombinant cationic biopolymers with high purity., Protein Expr Purif 134:11-17

 [3] Geitner AJ., Varga E., Wehmer M., Schmid FX., 2013, Generation of a highly active folding enzyme by combining a parvulin-type prolyl isomerase from SurA with an unrelated chaperone domain., J Mol Biol 425(22):4089-98

 [4] Haupt C., Patzschke R., Weininger U., Groger S., Kovermann M., Balbach J., 2011, Transient enzyme-substrate recognition monitored by real-time NMR., J Am Chem Soc 133(29):11154-62

 [5] Hu Y., Romao E., Vertommen D., Vincke C., Morales-Yanez F., Gutierrez C., Liu C., Muyldermans S., 2017, Generation of Nanobodies against SlyD and development of tools to eliminate this bacterial contaminant from recombinant proteins., Protein Expr Purif 137:64-76

 [6] Kovermann M., Balbach J., 2013, Dynamic control of the prolyl isomerase function of the dual-domain SlyD protein., Biophys Chem 171:16-23

 [7] Kovermann M., Zierold R., Haupt C., Low C., Balbach J., 2011, NMR relaxation unravels interdomain crosstalk of the two domain prolyl isomerase and chaperone SlyD., Biochim Biophys Acta 1814(7):873-81

 [8] Kumar A., Balbach J., 2017, Targeting the molecular chaperone SlyD to inhibit bacterial growth with a small molecule., Sci Rep 7:42141

 [9] Mokhonov VV., Vasilenko EA., Gorshkova EN., Astrakhantseva IV., Novikov DV., Novikov VV., 2018, SlyD-deficient Escherichia coli strains: A highway to contaminant-free protein extraction., Biochem Biophys Res Commun 499(4):967-972

 [10] Mukherjee S., Shukla A., Guptasarma P., 2003, Single-step purification of a protein-folding catalyst, the SlyD peptidyl prolyl isomerase (PPI), from cytoplasmic extracts of Escherichia coli., Biotechnol Appl Biochem 37(Pt 2):183-6

 [11] Zamble DB., 2015, Nickel in biology., Metallomics 7(4):588-9

 [12] Zhang F., Li B., Dong H., Chen M., Yao S., Li J., Zhang H., Liu X., Wang H., Song N., Zhang K., Du N., Xu S., Gu L., 2020, YdiV regulates Escherichia coli ferric uptake by manipulating the DNA-binding ability of Fur in a SlyD-dependent manner., Nucleic Acids Res

 [13] Zoldak G., Geitner AJ., Schmid FX., 2013, The prolyl isomerase SlyD is a highly efficient enzyme but decelerates the conformational folding of a client protein., J Am Chem Soc 135(11):4372-9

 [14] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [15] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78


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