MG_254_MONOMER – DNA ligase, NAD-dependent

Name
WID	MG_254_MONOMER
Name	DNA ligase, NAD-dependent
Cross references	PDB: 2OWO

Genetics
Gene	MG_254

Structure
Sequence	1 51 101 151 201 251 301 351 401 451 501 551 601 651 VMDVKLKIQQLVNLIKNYDYHYYVLSEPLIDDFEYDMLYKSLQQLEKDHP DLIQIDSPTQRVGGEAVKGFKKLNHNSPMLSLENAFSTKEIANFIDNINF QTNSKNEFVVEPKIDGVSISLTYKNGVLVHALTRGDGSVGEDVLNNVKTI KSIPLTIPFTKTIEIRGEIFVDKKTFLAINNQLEKPFANARNLAAGTIRN LNSEITAQRKLRALFYYIPNGLEESITTQTMVLEQLKQWKFPVSDTIRVF QNKFQLINYLEAFDKKREQLTFNLDGLVIKLNSLLFYQQLGATSKSPRWA IAFKFSPKFVQTKLTAVLITIGRTGRVNYTAKLESVNLDGTKVTAATLHN FDYIKTKDIRINDTVVIYKAGEIIPKVLKVNLEKRKNDTIIIQEQKYCPS CNSKLVKIVDEVDQYCTNETCKERNIQLINYFVSKTAMDINGLNINTITK LYEHNLVRSIVDLYDLKDKKNQVLKLDLKIGDKLFNKLVDNIENSKQKGM ARLLTGLGIKHVGNVLAKNLANHFKNIKALQHASLENLISLNDVGITVAE SLYNWFHDPNHLQLIEQLELRQVKTDQLPLKINFETNSIYFQKRFLITGS FNISRDQIKDLLSAKFDCQFASEVKPTVDFVIAGNKPTLRKINHAKELNI PIINEAIWT* 50 100 150 200 250 300 350 400 450 500 550 600 650 660
Is N‑terminal methionine cleaved	No
Prosthetic groups	(1) MG [c]
DNA footprint	Length: 19 (nt), Binding: dsDNA, Region: dsDNA
Empirical formula (pH 7.5)	H₅₄₈₄C₃₄₁₅N₉₀₅O₉₈₈S₁₁
Molecular weight (pH 7.5; Da)	75380.05
Extinction coefficient (260 nm, 25C, pH 7.0)	53915
Instability index	26.74
Is stable	True
Aliphatic index	104.55
GRAVY (25C, pH 7.0)	-0.250
Half life (OD (600 nm) = 0.3, M9 media, 36C; min)	1200

Synthesis
Localization	c

Function
Enzyme	DNA ligation [c]: (2) DR5P + NAD ⇒ AMP + dRibose5P_dRibose5P + H + NMN DNA ligationi [c]: (2) DR5P + NAD ⇒ AMP + dRibose5P_dRibose5P + H + NMN
Reaction participant	DNA bound protein release (DNA ligase, NAD-dependent releases DNA topoisomerase I) MG_122_MONOMER[d] + MG_254_MONOMER[c] ⇒ MG_122_MONOMER[c] + MG_254_MONOMER[d] DNA bound protein release (adenine-specific DNA modification methylase releases DNA ligase, NAD-dependent) MG_184_DIMER[c] + MG_254_MONOMER[d] ⇒ MG_184_DIMER[d] + MG_254_MONOMER[c] DNA bound protein release (DNA ligase, NAD-dependent releases DnaA-ATP 6mer) MG_254_MONOMER[c] + MG_469_6MER_ATP[d] ⇒ MG_254_MONOMER[d] + MG_469_6MER_ATP[c] DNA bound protein release (DNA ligase, NAD-dependent releases Spx subfamily protein) MG_127_MONOMER[d] + MG_254_MONOMER[c] ⇒ MG_127_MONOMER[c] + MG_254_MONOMER[d] DNA bound protein release (DNA ligase, NAD-dependent releases topoisomerase IV) MG_203_204_TETRAMER[d] + MG_254_MONOMER[c] ⇒ MG_203_204_TETRAMER[c] + MG_254_MONOMER[d] ... 41 more DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DNA ligase, NAD-dependent) MG_254_MONOMER[d] + MG_498_MONOMER[c] ⇒ MG_254_MONOMER[c] + MG_498_MONOMER[d] DNA bound protein release (DNA ligase, NAD-dependent releases Chromosome Segregation Protein SMC with SCP Proteins-ADP) MG_213_214_298_6MER_ADP[d] + MG_254_MONOMER[c] ⇒ MG_213_214_298_6MER_ADP[c] + MG_254_MONOMER[d] DNA bound protein release (DNA incision complex releases DNA ligase, NAD-dependent) MG_073_206_421_TETRAMER[c] + MG_254_MONOMER[d] ⇒ MG_073_206_421_TETRAMER[d] + MG_254_MONOMER[c] DNA bound protein release (DNA ligase, NAD-dependent releases DnaA-ATP 7mer) MG_254_MONOMER[c] + MG_469_7MER_ATP[d] ⇒ MG_254_MONOMER[d] + MG_469_7MER_ATP[c] DNA bound protein release (DNA ligase, NAD-dependent releases DnaA-ADP) MG_254_MONOMER[c] + MG_469_1MER_ADP[d] ⇒ MG_254_MONOMER[d] + MG_469_1MER_ADP[c] DNA bound protein release (Holliday junction endonuclease releases DNA ligase, NAD-dependent) MG_254_MONOMER[d] + MG_352_DIMER[c] ⇒ MG_254_MONOMER[c] + MG_352_DIMER[d] DNA bound protein release (type I restriction modification DNA specificity domain protein releases DNA ligase, NAD-dependent) MG_254_MONOMER[d] + MG_438_MONOMER[c] ⇒ MG_254_MONOMER[c] + MG_438_MONOMER[d] DNA bound protein release (DNA ligase, NAD-dependent releases DnaA-ATP) MG_254_MONOMER[c] + MG_469_1MER_ATP[d] ⇒ MG_254_MONOMER[d] + MG_469_1MER_ATP[c] DNA bound protein release (DNA ligase, NAD-dependent releases heat-inducible transcription repressor HrcA, putative) MG_205_DIMER[d] + MG_254_MONOMER[c] ⇒ MG_205_DIMER[c] + MG_254_MONOMER[d] DNA bound protein release (replicative DNA helicase releases DNA ligase, NAD-dependent) MG_094_HEXAMER[c] + MG_254_MONOMER[d] ⇒ MG_094_HEXAMER[d] + MG_254_MONOMER[c] DNA bound protein release (3-5' helicase releases DNA ligase, NAD-dependent) MG_244_DIMER[c] + MG_254_MONOMER[d] ⇒ MG_244_DIMER[d] + MG_254_MONOMER[c] DNA bound protein release (DNA ligase, NAD-dependent releases adenine-specific DNA modification methylase) MG_184_DIMER[d] + MG_254_MONOMER[c] ⇒ MG_184_DIMER[c] + MG_254_MONOMER[d] DNA bound protein release (DNA ligase, NAD-dependent releases single-strand binding protein family, octamer) MG_091_OCTAMER[d] + MG_254_MONOMER[c] ⇒ MG_091_OCTAMER[c] + MG_254_MONOMER[d] DNA bound protein release (DNA polymerase III, beta subunit releases DNA ligase, NAD-dependent) MG_001_MONOMER[c] + MG_254_MONOMER[d] ⇒ MG_001_MONOMER[d] + MG_254_MONOMER[c] DNA bound protein release (DNA ligase, NAD-dependent releases DNA-directed RNA polymerase holoenzyme) MG_254_MONOMER[c] + RNA_POLYMERASE_HOLOENZYME[d] ⇒ MG_254_MONOMER[d] + RNA_POLYMERASE_HOLOENZYME[c] DNA bound protein release (DNA ligase, NAD-dependent releases DnaA 6mer-(5)ATP-(1)ADP) MG_254_MONOMER[c] + MG_469_6MER_5ATP_ADP[d] ⇒ MG_254_MONOMER[d] + MG_469_6MER_5ATP_ADP[c] DNA bound protein release (recombination protein, strand exchange releases DNA ligase, NAD-dependent) MG_254_MONOMER[d] + MG_339_MONOMER[c] ⇒ MG_254_MONOMER[c] + MG_339_MONOMER[d] DNA bound protein release (DNA ligase, NAD-dependent releases DnaA 7mer-(6)ATP-(1)ADP) MG_254_MONOMER[c] + MG_469_7MER_6ATP_ADP[d] ⇒ MG_254_MONOMER[d] + MG_469_7MER_6ATP_ADP[c] DNA bound protein release (DNA ligase, NAD-dependent releases DNA-directed RNA polymerase) MG_254_MONOMER[c] + RNA_POLYMERASE[d] ⇒ MG_254_MONOMER[d] + RNA_POLYMERASE[c] DNA bound protein release (apurinic endonuclease releases DNA ligase, NAD-dependent) MG_235_MONOMER[c] + MG_254_MONOMER[d] ⇒ MG_235_MONOMER[d] + MG_254_MONOMER[c] DNA bound protein release (polI-like 5'-3' exonuclease, putative releases DNA ligase, NAD-dependent) MG_254_MONOMER[d] + MG_262_MONOMER[c] ⇒ MG_254_MONOMER[c] + MG_262_MONOMER[d] DNA bound protein release (DNA ligase, NAD-dependent releases LuxR bacterial regulatory protein, putative) MG_254_MONOMER[c] + MG_428_DIMER[d] ⇒ MG_254_MONOMER[d] + MG_428_DIMER[c] DNA bound protein release (DNA polymerase core, β-clamp, and primase releases DNA ligase, NAD-dependent) DNA_POLYMERASE_CORE_BETA_CLAMP_PRIMASE[c] + MG_254_MONOMER[d] ⇒ DNA_POLYMERASE_CORE_BETA_CLAMP_PRIMASE[d] + MG_254_MONOMER[c] DNA bound protein release (DNA ligase, NAD-dependent releases DnaA-ATP 2mer) MG_254_MONOMER[c] + MG_469_2MER_ATP[d] ⇒ MG_254_MONOMER[d] + MG_469_2MER_ATP[c] DNA bound protein release (DNA polymerase core, β-clamp, and γ-complex releases DNA ligase, NAD-dependent) DNA_POLYMERASE_CORE_BETA_CLAMP_GAMMA_COMPLEX[c] + MG_254_MONOMER[d] ⇒ DNA_POLYMERASE_CORE_BETA_CLAMP_GAMMA_COMPLEX[d] + MG_254_MONOMER[c] DNA bound protein release (DNA ligase, NAD-dependent releases DnaA 3mer-(2)ATP-(1)ADP) MG_254_MONOMER[c] + MG_469_3MER_2ATP_ADP[d] ⇒ MG_254_MONOMER[d] + MG_469_3MER_2ATP_ADP[c] DNA bound protein release (DNA polymerase (2) core, β-clamp, γ-complex, and primase releases DNA ligase, NAD-dependent) DNA_POLYMERASE_2CORE_BETA_CLAMP_GAMMA_COMPLEX_PRIMASE[c] + MG_254_MONOMER[d] ⇒ DNA_POLYMERASE_2CORE_BETA_CLAMP_GAMMA_COMPLEX_PRIMASE[d] + MG_254_MONOMER[c] DNA bound protein release (DNA ligase, NAD-dependent releases DnaA 5mer-(4)ATP-(1)ADP) MG_254_MONOMER[c] + MG_469_5MER_4ATP_ADP[d] ⇒ MG_254_MONOMER[d] + MG_469_5MER_4ATP_ADP[c] DNA bound protein release (DNA ligase, NAD-dependent releases DnaA 4mer-(3)ATP-(1)ADP) MG_254_MONOMER[c] + MG_469_4MER_3ATP_ADP[d] ⇒ MG_254_MONOMER[d] + MG_469_4MER_3ATP_ADP[c] DNA bound protein release (DNA ligase, NAD-dependent releases type I restriction modification DNA specificity domain protein) MG_254_MONOMER[c] + MG_438_MONOMER[d] ⇒ MG_254_MONOMER[d] + MG_438_MONOMER[c] DNA bound protein release (DNA ligase, NAD-dependent releases putative DNA integrity scanning protein) MG_105_OCTAMER[d] + MG_254_MONOMER[c] ⇒ MG_105_OCTAMER[c] + MG_254_MONOMER[d] DNA bound protein release (DNA ligase, NAD-dependent releases DnaA-ATP 5mer) MG_254_MONOMER[c] + MG_469_5MER_ATP[d] ⇒ MG_254_MONOMER[d] + MG_469_5MER_ATP[c] DNA bound protein release (Holliday junction DNA helicase releases DNA ligase, NAD-dependent) MG_254_MONOMER[d] + MG_358_359_10MER[c] ⇒ MG_254_MONOMER[c] + MG_358_359_10MER[d] DNA bound protein release (DNA ligase, NAD-dependent releases DnaA-ATP 4mer) MG_254_MONOMER[c] + MG_469_4MER_ATP[d] ⇒ MG_254_MONOMER[d] + MG_469_4MER_ATP[c] DNA bound protein release (uracil-DNA glycosylase, putative releases DNA ligase, NAD-dependent) MG_097_MONOMER[c] + MG_254_MONOMER[d] ⇒ MG_097_MONOMER[d] + MG_254_MONOMER[c] DNA bound protein release (DNA ligase, NAD-dependent releases DnaA 2mer-(1)ATP-(1)ADP) MG_254_MONOMER[c] + MG_469_2MER_1ATP_ADP[d] ⇒ MG_254_MONOMER[d] + MG_469_2MER_1ATP_ADP[c] DNA bound protein release (DNA polymerase III, beta clamp releases DNA ligase, NAD-dependent) MG_001_DIMER[c] + MG_254_MONOMER[d] ⇒ MG_001_DIMER[d] + MG_254_MONOMER[c] DNA bound protein release (DNA ligase, NAD-dependent releases DnaA-ATP 3mer) MG_254_MONOMER[c] + MG_469_3MER_ATP[d] ⇒ MG_254_MONOMER[d] + MG_469_3MER_ATP[c] DNA bound protein release (putative DNA integrity scanning protein releases DNA ligase, NAD-dependent) MG_105_OCTAMER[c] + MG_254_MONOMER[d] ⇒ MG_105_OCTAMER[d] + MG_254_MONOMER[c] DNA bound protein release (DNA ligase, NAD-dependent releases ferric uptake repressor) MG_236_MONOMER[d] + MG_254_MONOMER[c] ⇒ MG_236_MONOMER[c] + MG_254_MONOMER[d] DNA bound protein release (DNA ligase, NAD-dependent releases Uncharacterized HTH-type transcriptional regulator) MG_101_MONOMER[d] + MG_254_MONOMER[c] ⇒ MG_101_MONOMER[c] + MG_254_MONOMER[d]

Parameters
Parameters	Parameter_0111: ligaseRate = 0.04 1/s

Comments
Comments	Functional Macromolecule Functional as monomer [PUB_0333]. Coenzymes Interacts with 1 MG or MN per monomer as prosthetic group [387]. DNA-binding DNA footprint is 19 nt [PUB_0733].
References	Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW. Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications. EMBO J 19, 1119-29 (2000). WholeCell: PUB_0333, PubMed: 10698952 Shuman S. DNA ligases: progress and prospects. J Biol Chem 284, 17365-9 (2009). WholeCell: PUB_0733, PubMed: 19329793

Metadata
Created	2012-10-01 15:07:55
Last updated	2012-10-01 15:14:37