Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: peptidyl-prolyl cis-trans isomerase



Gene: fkpB Accession Numbers: EG11080 (EcoCyc), b0028, ECK0029

Synonyms: slpA, yaaD

Regulation Summary Diagram: ?

Summary:
FkpB is a peptidyl-prolyl cis-trans isomerase (PPIase) of the FK506-binding protein type [Hottenrott97]. FkpB also has chaperone activity; a number of ribosomal proteins appear to be natural substrates [Quistgaard12].

A crystal structure has been solved at 1.35 Å resolution. Serendipidously, the linker region of the purification tag of a symmetry-related mate polypeptide is found in the chaperone binding groove of the insert-in-flap (IF) domain of FkpB, mimicing a chaperone substrate [Quistgaard12].

SlpA: "SlyD-like protein" [Hottenrott97]

Citations: [Guo12a]

Gene Citations: [Tokunaga85, Regue84, Innis84, Miller87, Miller87a, Kamio85, Brissette91]

Locations: cytosol

Map Position: [25,826 -> 26,275] (0.56 centisomes)
Length: 450 bp / 149 aa

Molecular Weight of Polypeptide: 16.081 kD (from nucleotide sequence), 15.9 kD (experimental) [Hottenrott97 ]

Unification Links: ASAP:ABE-0000101 , DIP:DIP-35792N , EchoBASE:EB1072 , EcoGene:EG11080 , EcoliWiki:b0028 , OU-Microarray:b0028 , PortEco:fkpB , PR:PRO_000022634 , Pride:P0AEM0 , Protein Model Portal:P0AEM0 , RefSeq:NP_414569 , RegulonDB:EG11080 , SMR:P0AEM0 , String:511145.b0028 , UniProt:P0AEM0

Relationship Links: InterPro:IN-FAMILY:IPR001179 , InterPro:IN-FAMILY:IPR023566 , Panther:IN-FAMILY:PTHR10516 , PDB:Structure:4DT4 , Pfam:IN-FAMILY:PF00254 , Prosite:IN-FAMILY:PS50059

In Paralogous Gene Group: 8 (2 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0000413 - protein peptidyl-prolyl isomerization Inferred by computational analysis Inferred from experiment [Hottenrott97, UniProtGOA11a, GOA01]
GO:0061077 - chaperone-mediated protein folding Inferred from experiment Inferred by computational analysis [Gaudet10, Quistgaard12]
GO:0006457 - protein folding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0003755 - peptidyl-prolyl cis-trans isomerase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01, Hottenrott97]
GO:0005515 - protein binding Inferred from experiment [Quistgaard12]
GO:0005528 - FK506 binding Inferred by computational analysis [Gaudet10]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [Gaudet10]

MultiFun Terms: information transfer protein related chaperoning, repair (refolding)

Essentiality data for fkpB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Last-Curated ? 19-Feb-2014 by Keseler I , SRI International


Enzymatic reaction of: peptidyl-prolyl cis-trans isomerase

Synonyms: PPIase, peptide bond isomerase, peptidylproline cis-trans-isomerase, rotamase, peptidylprolyl isomerase

EC Number: 5.2.1.8

peptidylproline (ω = 180) <=> peptidylproline (ω = 0)

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[UniProt10a]
UniProt: Removed;
Conserved-Region 2 -> 72
[UniProt09]
UniProt: PPIase FKBP-type;
Chain 2 -> 149
[UniProt09]
UniProt: FKBP-type 16 kDa peptidyl-prolyl cis- trans isomerase;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0028 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11080; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Brissette91: Brissette JL, Weiner L, Ripmaster TL, Model P (1991). "Characterization and sequence of the Escherichia coli stress-induced psp operon." J Mol Biol 220(1);35-48. PMID: 1712397

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Guo12a: Guo W, Hao H, Dai M, Wang Y, Huang L, Peng D, Wang X, Wang H, Yao M, Sun Y, Liu Z, Yuan Z (2012). "Development of quinoxaline 1, 4-dioxides resistance in Escherichia coli and molecular change under resistance selection." PLoS One 7(8);e43322. PMID: 22952665

Hottenrott97: Hottenrott S, Schumann T, Pluckthun A, Fischer G, Rahfeld JU (1997). "The Escherichia coli SlyD is a metal ion-regulated peptidyl-prolyl cis/trans-isomerase." J Biol Chem 272(25);15697-701. PMID: 9188461

Innis84: Innis MA, Tokunaga M, Williams ME, Loranger JM, Chang SY, Chang S, Wu HC (1984). "Nucleotide sequence of the Escherichia coli prolipoprotein signal peptidase (lsp) gene." Proc Natl Acad Sci U S A 81(12);3708-12. PMID: 6374664

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kamio85: Kamio Y, Lin CK, Regue M, Wu HC (1985). "Characterization of the ileS-lsp operon in Escherichia coli. Identification of an open reading frame upstream of the ileS gene and potential promoter(s) for the ileS-lsp operon." J Biol Chem 260(9);5616-20. PMID: 2985604

Miller87: Miller KW, Wu HC (1987). "Cotranscription of the Escherichia coli isoleucyl-tRNA synthetase (ileS) and prolipoprotein signal peptidase (lsp) genes. Fine-structure mapping of the lsp internal promoter." J Biol Chem 262(1);389-93. PMID: 2432063

Miller87a: Miller KW, Bouvier J, Stragier P, Wu HC (1987). "Identification of the genes in the Escherichia coli ileS-lsp operon. Analysis of multiple polycistronic mRNAs made in vivo." J Biol Chem 262(15);7391-7. PMID: 3294831

Quistgaard12: Quistgaard EM, Nordlund P, Low C (2012). "High-resolution insights into binding of unfolded polypeptides by the PPIase chaperone SlpA." FASEB J 26(10);4003-13. PMID: 22735173

Regue84: Regue M, Remenick J, Tokunaga M, Mackie GA, Wu HC (1984). "Mapping of the lipoprotein signal peptidase gene (lsp)." J Bacteriol 158(2);632-5. PMID: 6373724

Tokunaga85: Tokunaga M, Loranger JM, Chang SY, Regue M, Chang S, Wu HC (1985). "Identification of prolipoprotein signal peptidase and genomic organization of the lsp gene in Escherichia coli." J Biol Chem 260(9);5610-5. PMID: 2580835

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

Bouvier91a: Bouvier J, Stragier P (1991). "Nucleotide sequence of the lsp-dapB interval in Escherichia coli." Nucleic Acids Res 19(1);180. PMID: 2011499

Nonaka06: Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA (2006). "Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress." Genes Dev 20(13);1776-89. PMID: 16818608


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Dec 19, 2014, BIOCYC14B.