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Escherichia coli K-12 substr. MG1655 Enzyme: DNA ligase



Gene: ligB Accession Numbers: EG11334 (EcoCyc), b3647, ECK3637

Synonyms: yicF

Regulation Summary Diagram: ?

Summary:
LigB is an NAD(+)-dependent DNA ligase [Sriskanda01]. LigB has similarity to LigA, the other NAD(+)-dependent DNA ligase in E. coli [Sriskanda01].

The reaction requires divalent cations which can be magnesium, manganese, or cobalt [Sriskanda01]. A ligase-adenylate intermediate has been characterized [Sriskanda01]. LigB lacks the BRCT domain and 2 of the 4 zinc-binding cysteines that are characteristic of bacterial NAD+ ligases. LigB has less nick-joining activity than LigA both in vivo and in vitro [Sriskanda01].

A K126A mutation eliminates the enzyme activity [Sriskanda01].

ligB mRNA transcripts showed an unusual decrease in polyadenylation in a PAP I overexpressing strain [Mohanty06].

Locations: cytosol

Map Position: [3,817,511 <- 3,819,193] (82.28 centisomes)
Length: 1683 bp / 560 aa

Molecular Weight of Polypeptide: 63.179 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011923 , EchoBASE:EB1310 , EcoGene:EG11334 , EcoliWiki:b3647 , ModBase:P25772 , OU-Microarray:b3647 , PortEco:ligB , PR:PRO_000023090 , Pride:P25772 , Protein Model Portal:P25772 , RefSeq:NP_418104 , RegulonDB:EG11334 , SMR:P25772 , String:511145.b3647 , UniProt:P25772

Relationship Links: InterPro:IN-FAMILY:IPR004150 , InterPro:IN-FAMILY:IPR010994 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR013839 , InterPro:IN-FAMILY:IPR013840 , InterPro:IN-FAMILY:IPR018239 , InterPro:IN-FAMILY:IPR020923 , Pfam:IN-FAMILY:PF01653 , Pfam:IN-FAMILY:PF03120 , Prosite:IN-FAMILY:PS01055 , Prosite:IN-FAMILY:PS01056 , Smart:IN-FAMILY:SM00532

In Paralogous Gene Group: 547 (2 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006266 - DNA ligation Inferred from experiment [Sriskanda01]
GO:0006259 - DNA metabolic process Inferred by computational analysis [GOA06, GOA01a]
GO:0006260 - DNA replication Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0006281 - DNA repair Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0006288 - base-excision repair, DNA ligation Inferred by computational analysis [Gaudet10]
GO:0006974 - cellular response to DNA damage stimulus Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003911 - DNA ligase (NAD+) activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Sriskanda01]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [Gaudet10]

MultiFun Terms: information transfer DNA related

Essentiality data for ligB 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 ? 13-May-2008 by Johnson A , JCVI


Enzymatic reaction of: DNA ligase

Synonyms: DNA ligase (NAD+), polydeoxyribonucleotide synthase (NAD)

EC Number: 6.5.1.-

(deoxynucleotides)(m) + (deoxynucleotides)(n) + NAD+ <=> (deoxynucleotides)(n+m) + β-nicotinamide D-ribonucleotide + AMP

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Cofactors or Prosthetic Groups: Mg2+ [Sriskanda01]

Kinetic Parameters:

Substrate
Km (μM)
Citations
NAD+
0.03
[Maunders93, BRENDA14]
NAD+
3.0
[Sriskanda99, BRENDA14]

T(opt): 10 °C [BRENDA14, Maunders93], 25 °C [BRENDA14, Lim01a], 40 °C [BRENDA14, He11a]

pH(opt): 7.5 [BRENDA14, Maunders93], 8 [BRENDA14, Maunders93]


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 124
[Sriskanda01, UniProt11a]
Alternate sequence: K → A; UniProt: Loss of activity.
Active-Site 124
[UniProt10]
UniProt: N6-AMP-lysine intermediate; Non-Experimental Qualifier: probable;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b3647 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11334; 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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

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."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

He11a: He X, Ni X, Wang Y, Wang K, Jian L (2011). "Electrochemical detection of nicotinamide adenine dinucleotide based on molecular beacon-like DNA and E. coli DNA ligase." Talanta 83(3);937-42. PMID: 21147340

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

Lim01a: Lim JH, Choi J, Han SJ, Kim SH, Hwang HZ, Jin DK, Ahn BY, Han YS (2001). "Molecular cloning and characterization of thermostable DNA ligase from Aquifex pyrophilus, a hyperthermophilic bacterium." Extremophiles 5(3);161-8. PMID: 11453459

Maunders93: Maunders MJ (1993). "DNA and RNA ligases (EC 6.5.1.1, EC 6.5.1.2, and EC 6.5.1.3)." Methods Mol Biol 16;213-30. PMID: 19082974

Mohanty06: Mohanty BK, Kushner SR (2006). "The majority of Escherichia coli mRNAs undergo post-transcriptional modification in exponentially growing cells." Nucleic Acids Res 34(19);5695-704. PMID: 17040898

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Sriskanda01: Sriskanda V, Shuman S (2001). "A second NAD(+)-dependent DNA ligase (LigB) in Escherichia coli." Nucleic Acids Res 29(24);4930-4. PMID: 11812821

Sriskanda99: Sriskanda V, Schwer B, Ho CK, Shuman S (1999). "Mutational analysis of Escherichia coli DNA ligase identifies amino acids required for nick-ligation in vitro and for in vivo complementation of the growth of yeast cells deleted for CDC9 and LIG4." Nucleic Acids Res 27(20);3953-63. PMID: 10497258

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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


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 Sun Nov 23, 2014, BIOCYC13A.