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discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
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Escherichia coli K-12 substr. MG1655 Polypeptide: YdcU



Gene: ydcU Accession Numbers: G6753 (EcoCyc), b1442, ECK1436

Regulation Summary Diagram: ?

Component of: YdcS/YdcT/YdcV/YdcU ABC transporter (summary available)

Summary:
YdcU is a membrane component of a predicted spermidine/putrescine ABC transporter.

Gene Citations: [Schneider13, Zimmer00]

Locations: inner membrane

Map Position: [1,511,855 -> 1,512,796] (32.59 centisomes)
Length: 942 bp / 313 aa

Molecular Weight of Polypeptide: 34.36 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004807 , EchoBASE:EB3527 , EcoGene:EG13764 , EcoliWiki:b1442 , OU-Microarray:b1442 , PortEco:ydcU , Protein Model Portal:P77156 , RefSeq:NP_415959 , RegulonDB:G6753 , String:511145.b1442 , UniProt:P77156

Relationship Links: InterPro:IN-FAMILY:IPR000515 , Pfam:IN-FAMILY:PF00528 , Prosite:IN-FAMILY:PS50928

In Paralogous Gene Group: 24 (43 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006810 - transport Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: cell structure membrane
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, membrane component

Essentiality data for ydcU knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]
Yes [Feist07, Comment 3]

Subunit of: YdcS/YdcT/YdcV/YdcU ABC transporter

Subunit composition of YdcS/YdcT/YdcV/YdcU ABC transporter = [YdcS][YdcT]2[YdcV][YdcU]

Summary:
YdcS, YdcT, YdcU and YdcV are uncharacterized members of the ABC superfamily of transporters [Saurin99]. YdcS is the putative periplasmic binding component, YdcT is the putative ATP binding component, YdcU and YdcV are the putative membrane spanning components. Bases on sequence similarity they may function together as an ATP-dependent spermidine/ putrescine transporter. The genes ydcS, ydcT, ydcU, and ydcV are probably located in a single operon.


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 26 -> 46
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Conserved-Region 87 -> 302
[UniProt09]
UniProt: ABC transmembrane type-1;
Transmembrane-Region 93 -> 113
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 123 -> 143
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 155 -> 175
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 188 -> 208
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 231 -> 251
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 253 -> 273
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 284 -> 304
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

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

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

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

Saurin99: Saurin W, Hofnung M, Dassa E (1999). "Getting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters." J Mol Evol 1999;48(1);22-41. PMID: 9873074

Schneider13: Schneider BL, Hernandez VJ, Reitzer L (2013). "Putrescine catabolism is a metabolic response to several stresses in Escherichia coli." Mol Microbiol 88(3);537-50. PMID: 23531166

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

UniProt10: 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."

Zimmer00: Zimmer DP, Soupene E, Lee HL, Wendisch VF, Khodursky AB, Peter BJ, Bender RA, Kustu S (2000). "Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation." Proc Natl Acad Sci U S A 97(26);14674-9. PMID: 11121068


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 Sat Dec 20, 2014, biocyc12.