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Escherichia coli K-12 substr. MG1655 Polypeptide: peptide ABC transporter - periplasmic binding protein



Gene: oppA Accession Numbers: EG10674 (EcoCyc), b1243, ECK1237

Regulation Summary Diagram: ?

Component of: peptide ABC transporter OppABCDF (extended summary available)

Summary:
Resequencing of multiple isolates of the MG1655 strain has identified several genetic variations compared to the reference sequence, including an IS5 insertion in the region upstream of oppA which may alter its regulation [Freddolino12]. This EcoliWiki page summarizes these sequence differences.

oppA shows differential codon adaptation, resulting in differential translation efficiency signatures, in thermophilic microbes. It was therefore predicted to play a role in the heat shock response. A oppA deletion mutant was shown to be more sensitive than wild-type specifically to heat shock, but not other stresses [Krisko14].

Gene Citations: [Andrews86, Hiles87]

Locations: periplasmic space

Map Position: [1,299,206 -> 1,300,837] (28.0 centisomes)
Length: 1632 bp / 543 aa

Molecular Weight of Polypeptide: 60.899 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004172 , CGSC:18094 , DIP:DIP-10405N , EchoBASE:EB0668 , EcoGene:EG10674 , EcoliWiki:b1243 , ModBase:P23843 , OU-Microarray:b1243 , PortEco:oppA , PR:PRO_000023461 , Pride:P23843 , Protein Model Portal:P23843 , RefSeq:NP_415759 , RegulonDB:EG10674 , SMR:P23843 , String:511145.b1243 , Swiss-Model:P23843 , UniProt:P23843

Relationship Links: InterPro:IN-FAMILY:IPR000914 , InterPro:IN-FAMILY:IPR023765 , PDB:Structure:3TCF , PDB:Structure:3TCG , PDB:Structure:3TCH , Pfam:IN-FAMILY:PF00496 , Prosite:IN-FAMILY:PS01040

In Paralogous Gene Group: 25 (11 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006857 - oligopeptide transport Inferred from experiment [Guyer85]
GO:0009408 - response to heat Inferred from experiment [Krisko14]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0015031 - protein transport Inferred by computational analysis [UniProtGOA11a]
GO:0015833 - peptide transport Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0005215 - transporter activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space Inferred from experiment Inferred by computational analysis [DiazMejia09, Han13, Zhang07, Molloy00, LopezCampistrou05]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: cell structure murein
metabolism central intermediary metabolism murein turnover, recycling
transport Channel-type Transporters Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases ABC superfamily, periplasmic binding component

Essentiality data for oppA 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]
Yes [Feist07, Comment 4]

Subunit of: peptide ABC transporter OppABCDF

Subunit composition of peptide ABC transporter OppABCDF = [OppC][OppD][OppF][OppB][OppA]
         murein tripeptide ABC transporter / peptide ABC transporter - putative membrane subunit = OppC (summary available)
         murein tripeptide ABC transporter / peptide ABC transporter - putative ATP binding subunit = OppD (summary available)
         murein tripeptide ABC transporter / peptide ABC transporter - putative ATP binding subunit = OppF (summary available)
         murein tripeptide ABC transporter / peptide ABC transporter - putative membrane subunit = OppB (summary available)
         peptide ABC transporter - periplasmic binding protein = OppA (summary available)

Summary:
OppABCDF is an ATP-dependent oligopeptide transporter that is a member of the ATP-Binding Cassette (ABC) Superfamily of transporters [Pearce92]. OppABCDF has not been investigated in detail in E. coli, but the orthologous system in Salmonella typhimurium has been extensively characterized. Binding affinity and competition assays have shown that OppABCDF will transport oligopeptides up to five amino acids in length, but has no affinity for free amino acids [Guyer86]. The system has been observed to function in oligopeptide uptake, as well as recycling of cell wall peptides [Hiles87, Goodell87]. Based on sequence similarity, OppB and OppC are the membrane components of the ABC transporter, and OppD and OppF are the ATP-binding components of the ABC transporter [Pearce92]. OppA is the periplasmic substrate-binding component that binds oligopeptides with a Kd of approximately 1E-6 [Tame94]. Insertion mutant of the oppF gene has shown that OppF is required for Opp transporter function [Hiles87]. In addition, insertional mutants of each of the opp genes were constructed, and the opp-minus strains were unable to utilize the peptide Pro-Gly-Gly, normally transported by the wild-type transporter [Hiles87].

OppA has been crystallized and its structure resolved to 2.3 A resolution showing OppA to be a bilobal, principally beta-stranded, three-domain protein [Glover95].

Targeting of OppA to the Sec-translocase for transport across the inner membrane is SecB-dependent [Baars06].


Enzymatic reaction of: transport of a peptide (peptide ABC transporter OppABCDF)


Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 26
[Pasquali94, Wilkins98, Link97, Urbanowski00]
 
Chain 27 -> 543
[UniProt09]
UniProt: Periplasmic oligopeptide-binding protein;
Sequence-Conflict 271
[Pahel93, UniProt10]
Alternate sequence: N → Y; UniProt: (in Ref. 2; AAA21302);
Disulfide-Bond-Site 443, 297
[UniProt10a]
UniProt: Non-Experimental Qualifier: by similarity;
Sequence-Conflict 314 -> 315
[Pahel93, UniProt10]
Alternate sequence: RV → LW; UniProt: (in Ref. 2; AAA21302);
Sequence-Conflict 487 -> 488
[Pahel93, UniProt10]
Alternate sequence: QR → HG; UniProt: (in Ref. 2; AAA21302);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Suzanne Paley on Thu Oct 21, 2004:
Position updated based on U00096.2 release of genome
10/20/97 Gene b1243 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10674; confirmed by SwissProt match.


References

Andrews86: Andrews JC, Short SA (1986). "opp-lac Operon fusions and transcriptional regulation of the Escherichia coli trp-linked oligopeptide permease." J Bacteriol 1986;165(2);434-42. PMID: 3080404

Baars06: Baars L, Ytterberg AJ, Drew D, Wagner S, Thilo C, van Wijk KJ, de Gier JW (2006). "Defining the role of the Escherichia coli chaperone SecB using comparative proteomics." J Biol Chem 281(15);10024-34. PMID: 16352602

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

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Freddolino12: Freddolino PL, Amini S, Tavazoie S (2012). "Newly identified genetic variations in common Escherichia coli MG1655 stock cultures." J Bacteriol 194(2);303-6. PMID: 22081388

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

Glover95: Glover ID (1995). "Structure determination of OppA at 2.3 A resolution using multiple-wavelength anomalous dispersion methods." Acta Crystallogr D Biol Crystallogr 51(Pt 1);39-47. PMID: 15299334

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

Goodell87: Goodell EW, Higgins CF (1987). "Uptake of cell wall peptides by Salmonella typhimurium and Escherichia coli." J Bacteriol 169(8);3861-5. PMID: 3301822

Guyer85: Guyer CA, Morgan DG, Osheroff N, Staros JV (1985). "Purification and characterization of a periplasmic oligopeptide binding protein from Escherichia coli." J Biol Chem 260(19);10812-8. PMID: 3897225

Guyer86: Guyer CA, Morgan DG, Staros JV (1986). "Binding specificity of the periplasmic oligopeptide-binding protein from Escherichia coli." J Bacteriol 1986;168(2);775-9. PMID: 3536860

Han13: Han MJ, Kim JY, Kim JA (2013). "Comparison of the large-scale periplasmic proteomes of the Escherichia coli K-12 and B strains." J Biosci Bioeng. PMID: 24140104

Hiles87: Hiles ID, Gallagher MP, Jamieson DJ, Higgins CF (1987). "Molecular characterization of the oligopeptide permease of Salmonella typhimurium." J Mol Biol 1987;195(1);125-42. PMID: 2821267

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

Krisko14: Krisko A, Copi T, Gabaldon T, Lehner B, Supek F (2014). "Inferring gene function from evolutionary change in signatures of translation efficiency." Genome Biol 15(3);R44. PMID: 24580753

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Molloy00: Molloy MP, Herbert BR, Slade MB, Rabilloud T, Nouwens AS, Williams KL, Gooley AA (2000). "Proteomic analysis of the Escherichia coli outer membrane." Eur J Biochem 267(10);2871-81. PMID: 10806384

Pahel93: Pahel G., Short S.A. (1993). Data submission to EMBL/GenBank/DDBJ databases on 1993-07.

Pasquali94: Pasquali C., Sanchez J.-C., Ravier F., Golaz O., Hughes G.J., Frutiger S., Paquet N., Wilkins M., Appel R.D., Bairoch A., Hochstrasser D.F. (1994). Data submission to UniProtKB on 1994-09.

Pearce92: Pearce SR, Mimmack ML, Gallagher MP, Gileadi U, Hyde SC, Higgins CF (1992). "Membrane topology of the integral membrane components, OppB and OppC, of the oligopeptide permease of Salmonella typhimurium." Mol Microbiol 1992;6(1);47-57. PMID: 1738314

Tame94: Tame JR, Murshudov GN, Dodson EJ, Neil TK, Dodson GG, Higgins CF, Wilkinson AJ (1994). "The structural basis of sequence-independent peptide binding by OppA protein." Science 1994;264(5165);1578-81. PMID: 8202710

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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

Urbanowski00: Urbanowski ML, Stauffer LT, Stauffer GV (2000). "The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." Mol Microbiol 37(4);856-68. PMID: 10972807

Wilkins98: Wilkins MR, Gasteiger E, Tonella L, Ou K, Tyler M, Sanchez JC, Gooley AA, Walsh BJ, Bairoch A, Appel RD, Williams KL, Hochstrasser DF (1998). "Protein identification with N and C-terminal sequence tags in proteome projects." J Mol Biol 278(3);599-608. PMID: 9600841

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

Other References Related to Gene Regulation

Andrews86a: Andrews JC, Blevins TC, Short SA (1986). "Regulation of peptide transport in Escherichia coli: induction of the trp-linked operon encoding the oligopeptide permease." J Bacteriol 1986;165(2);428-33. PMID: 3511033

Chen07: Chen Z, Lewis KA, Shultzaberger RK, Lyakhov IG, Zheng M, Doan B, Storz G, Schneider TD (2007). "Discovery of Fur binding site clusters in Escherichia coli by information theory models." Nucleic Acids Res 35(20);6762-77. PMID: 17921503

Fraenkel95: Fraenkel YM, Mandel Y, Friedberg D, Margalit H (1995). "Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon." Comput Appl Biosci 1995;11(4);379-87. PMID: 8521047

GamaCastro08: Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, Bonavides-Martinez C, Abreu-Goodger C, Rodriguez-Penagos C, Miranda-Rios J, Morett E, Merino E, Huerta AM, Trevino-Quintanilla L, Collado-Vides J (2008). "RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation." Nucleic Acids Res 36(Database issue);D120-4. PMID: 18158297

Higashi08a: Higashi K, Terui Y, Suganami A, Tamura Y, Nishimura K, Kashiwagi K, Igarashi K (2008). "Selective Structural Change by Spermidine in the Bulged-out Region of Double-stranded RNA and Its Effect on RNA Function." J Biol Chem 283(47);32989-94. PMID: 18824545

Pulvermacher08: Pulvermacher SC, Stauffer LT, Stauffer GV (2008). "The role of the small regulatory RNA GcvB in GcvB/mRNA posttranscriptional regulation of oppA and dppA in Escherichia coli." FEMS Microbiol Lett 281(1);42-50. PMID: 18312576

Salmon05: Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, Hatfield GW, Gunsalus RP (2005). "Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA." J Biol Chem 280(15);15084-96. PMID: 15699038

Tao05: Tao H, Hasona A, Do PM, Ingram LO, Shanmugam KT (2005). "Global gene expression analysis revealed an unsuspected deo operon under the control of molybdate sensor, ModE protein, in Escherichia coli." Arch Microbiol 184(4);225-33. PMID: 16205910

Yoshida99: Yoshida M, Meksuriyen D, Kashiwagi K, Kawai G, Igarashi K (1999). "Polyamine stimulation of the synthesis of oligopeptide-binding protein (OppA). Involvement of a structural change of the Shine-Dalgarno sequence and the initiation codon aug in oppa mRNA." J Biol Chem 274(32);22723-8. PMID: 10428855


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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 Sat Dec 20, 2014, biocyc14.