ligB:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

LigB

Synonyms

DNA ligase, NAD(+)-dependent[1], B3647[2][1], LigB[2][1], YicF[2][1] , ECK3637, JW3622, yicF, b3647

Product description

DNA ligase[2][3]

DNA ligase B, NAD(+)-dependent[4]

EC number (for enzymes)


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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0000287

magnesium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc (v14.0)

complete

GO:0003911

DNA ligase (NAD+) activity

PMID:11812821[5]

IDA: Inferred from Direct Assay

F

complete

GO:0003911

DNA ligase (NAD+) activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01587

F

Seeded from EcoCyc (v14.0)

complete

GO:0003911

DNA ligase (NAD+) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004150

F

Seeded from EcoCyc (v14.0)

complete

GO:0003911

DNA ligase (NAD+) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013839

F

Seeded from EcoCyc (v14.0)

complete

GO:0003911

DNA ligase (NAD+) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013840

F

Seeded from EcoCyc (v14.0)

complete

GO:0003911

DNA ligase (NAD+) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018239

F

Seeded from EcoCyc (v14.0)

complete

GO:0003911

DNA ligase (NAD+) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020923

F

Seeded from EcoCyc (v14.0)

complete

GO:0003911

DNA ligase (NAD+) activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:6.5.1.2

F

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004150

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018239

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0235

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004150

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018239

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0234

P

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0227

P

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

F

Seeded from EcoCyc (v14.0)

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MMMKVWMAIL IGILCWQSSV WAVCPAWSPA RAQEEISRLQ QQIKQWDDDY WKEGKSEVED
GVYDQLSARL TQWQRCFGSE PRDVMMPPLN GAVMHPVAHT GVRKMVDKNA LSLWMRERSD
LWVQPKVDGV AVTLVYRDGK LNKAISRGNG LKGEDWTQKV SLISAVPQTV SGPLANSTLQ
GEIFLQREGH IQQQMGGINA RAKVAGLMMR QDDSDTLNSL GVFVWAWPDG PQLMSDRLKE
LATAGFTLTQ TYTRAVKNAD EVARVRNEWW KAELPFVTDG VVVRAAKEPE SRHWLPGQAE
WLVAWKYQPV AQVAEVKAIQ FAVGKSGKIS VVASLAPVML DDKKVQRVNI GSVRRWQEWD
IAPGDQILVS LAGQGIPRID DVVWRGAERT KPTPPENRFN SLTCYFASDV CQEQFISRLV
WLGAKQVLGL DGIGEAGWRA LHQTHRFEHI FSWLLLTPEQ LQNTPGIAKS KSAQLWHQFN
LARKQPFTRW VMAMGIPLTR AALNASDERS WSQLLFSTEQ FWQQLPGTGS GRARQVIEWK
ENAQIKKLGS WLAAQQITGF EP
Length

562

Mol. Wt

63.44 kDa

pI

9.3 (calculated)

Extinction coefficient

168,440 - 169,065 (calc based on 6 Y, 29 W, and 5 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

28..308

PF01653 NAD-dependent DNA ligase adenylation domain

PMID:19920124[6]

Domain

310..393

PF03120 NAD-dependent DNA ligase OB-fold domain

PMID:19920124[6]

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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=ligB taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:90111628

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948164

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011923

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P25772

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11334

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11334

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948164

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001305

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1310

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ Sriskanda, V & Shuman, S (2001) A second NAD(+)-dependent DNA ligase (LigB) in Escherichia coli. Nucleic Acids Res. 29 4930-4 PubMed
  6. ↑ 6.0 6.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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