Escherichia coli K-12 substr. MG1655 Polypeptide: ATP-binding protein with possible role in replication

Gene: uup Accession Numbers: G6489 (EcoCyc), b0949, ECK0940

Synonyms: ycbI, ycbH, tex

Regulation Summary Diagram: ?

Regulation summary diagram for uup

Uup is a cytosolic ATP-binding cassette (ABC) protein belonging to the REG subfamily [Reddy97, Kerr04, Murat06]. The physiological role of the wild-type protein is not yet known, but a role in replication fork progression has been suggested [Murat06].

The purified Uup protein binds and hydrolyzes ATP, leading to a large conformational change in its C-terminal DNA binding domain. The ATPase activity of Uup is strongly inhibited by 0.5 mM N-ethyl maleimide, but is insensitive to vanadate [Murat06]. ATPase function is required for the function of Uup in vivo [Murat06, Murat08].

The DNA-binding activity of Uup does not appear to be sequence specific [Murat06]. The C-terminal domain of Uup, which has similarity to the "little finger" domain of the Y family of DNA polymerases, contributes to DNA binding activity and is essential for the effect of Uup on the frequency of transposon excision [Burgos10]. A solution structure of the C-terminal domain indicates the presence of three α-helices and suggests that the domain forms an intramolecular antiparallel two-stranded coiled coil [Carlier12, Carlier12a].

Mutations in the uup gene cause an increase in RecA-independent precise excision of transposons [Hopkins83, Reddy97, Reddy00] and decreased growth of bacteriophage Mu [Hopkins83, Reddy00]. Deletion of uup leads to cell contact-dependent decrease in viability when the mutant is co-cultured with the wild type parent [Murat08]. uup insertion mutants were identified in a genetic screen for genes that are important for survival of exposure to ionizing radiation (IR). A uup deletion mutant has a moderate decrease in IR survival [Byrne14].

uup is expressed as the downstream gene in an operon together with ycbY; expression is constitutive at a moderate level [Reddy00].

Tex: "transposon excision" [Reddy97]

Locations: inner membrane, cytosol

Map Position: [1,009,187 -> 1,011,094] (21.75 centisomes, 78°)
Length: 1908 bp / 635 aa

Molecular Weight of Polypeptide: 72.067 kD (from nucleotide sequence), 73 kD (experimental) [Reddy00 ]

Unification Links: ASAP:ABE-0003213 , DIP:DIP-11099N , EchoBASE:EB2933 , EcoGene:EG13134 , EcoliWiki:b0949 , Mint:MINT-1228036 , ModBase:P43672 , OU-Microarray:b0949 , PortEco:uup , PR:PRO_000024197 , Pride:P43672 , Protein Model Portal:P43672 , RefSeq:NP_415469 , RegulonDB:G6489 , SMR:P43672 , String:511145.b0949 , UniProt:P43672

Relationship Links: InterPro:IN-FAMILY:IPR003439 , InterPro:IN-FAMILY:IPR003593 , InterPro:IN-FAMILY:IPR017871 , InterPro:IN-FAMILY:IPR027417 , PDB:Structure:2LW1 , Pfam:IN-FAMILY:PF00005 , Prosite:IN-FAMILY:PS00211 , Prosite:IN-FAMILY:PS50893 , Smart:IN-FAMILY:SM00382

In Paralogous Gene Group: 23 (75 members)

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred from experiment Inferred by computational analysis [GOA01a, Murat06]
GO:0070894 - regulation of transposon integration Inferred from experiment [Hopkins83]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment [Murat06]
GO:0016887 - ATPase activity Inferred from experiment Inferred by computational analysis [GOA01a, Murat06]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Murat06]
GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [DiazMejia09, Zhang07]

MultiFun Terms: extrachromosomal prophage genes and phage related functions
extrachromosomal transposon related

Essentiality data for uup 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]

Last-Curated ? 01-Aug-2014 by Keseler I , SRI International

Sequence Features

Protein sequence of ATP-binding protein with possible role in replication with features indicated

Feature Class Location Citations Comment
Conserved-Region 1 -> 253
UniProt: ABC transporter 1;
Nucleotide-Phosphate-Binding-Region 36 -> 43
UniProt: ATP 1; Non-Experimental Qualifier: potential;
Conserved-Region 320 -> 546
UniProt: ABC transporter 2;
Nucleotide-Phosphate-Binding-Region 352 -> 359
UniProt: ATP 2; Non-Experimental Qualifier: potential;
Protein-Segment 547 -> 552
UniProt: Poly-Ala; Sequence Annotation Type: compositionally biased region;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


3/2/1998 (pkarp) Merged genes G294/EG13134 and G6489/uup
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

Burgos10: Burgos Zepeda MY, Alessandri K, Murat D, El Amri C, Dassa E (2010). "C-terminal domain of the Uup ATP-binding cassette ATPase is an essential folding domain that binds to DNA." Biochim Biophys Acta 1804(4);755-61. PMID: 19948254

Byrne14: Byrne RT, Chen SH, Wood EA, Cabot EL, Cox MM (2014). "Escherichia coli genes and pathways involved in surviving extreme exposure to ionizing radiation." J Bacteriol 196(20);3534-45. PMID: 25049088

Carlier12: Carlier L, Haase AS, Burgos Zepeda MY, Dassa E, Lequin O (2012). "Secondary structure and NMR resonance assignments of the C-terminal DNA-binding domain of Uup protein." Biomol NMR Assign 6(2);197-200. PMID: 22287065

Carlier12a: Carlier L, Haase AS, Burgos Zepeda MY, Dassa E, Lequin O (2012). "The C-terminal domain of the Uup protein is a DNA-binding coiled coil motif." J Struct Biol 180(3);577-84. PMID: 22995754

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

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

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

Hopkins83: Hopkins JD, Clements M, Syvanen M (1983). "New class of mutations in Escherichia coli (uup) that affect precise excision of insertion elements and bacteriophage Mu growth." J Bacteriol 1983;153(1);384-9. PMID: 6294054

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

Kerr04: Kerr ID (2004). "Sequence analysis of twin ATP binding cassette proteins involved in translational control, antibiotic resistance, and ribonuclease L inhibition." Biochem Biophys Res Commun 315(1);166-73. PMID: 15013441

Murat06: Murat D, Bance P, Callebaut I, Dassa E (2006). "ATP hydrolysis is essential for the function of the UUP ABC ATPASE in precise excision of transposons." J Biol Chem 281(10):6850-9. PMID: 16407313

Murat08: Murat D, Goncalves L, Dassa E (2008). "Deletion of the Escherichia coli uup gene encoding a protein of the ATP binding cassette superfamily affects bacterial competitiveness." Res Microbiol 159(9-10);671-7. PMID: 18848624

Reddy00: Reddy M, Gowrishankar J (2000). "Characterization of the uup locus and its role in transposon excisions and tandem repeat deletions in Escherichia coli." J Bacteriol 182(7);1978-86. PMID: 10715006

Reddy97: Reddy M, Gowrishankar J (1997). "Identification and characterization of ssb and uup mutants with increased frequency of precise excision of transposon Tn10 derivatives: nucleotide sequence of uup in Escherichia coli." J Bacteriol 1997;179(9);2892-9. PMID: 9139905

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.

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

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

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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 19.0 on Tue Jul 7, 2015, biocyc13.