Probable DNA ligase - Mycobacterium tuberculosis H37Rv

Preferred order of sections

Names and origin

Protein names

Recommended name:
Probable DNA ligase HAMAP-Rule MF_00407
EC=6.5.1.1 HAMAP-Rule MF_00407

Alternative name(s):
Polydeoxyribonucleotide synthase [ATP] HAMAP-Rule MF_00407

Gene names

Name:	lig HAMAP-Rule MF_00407
ORF Names:	RVBD_3062 EMBL AFN51052.1

Organism

Mycobacterium tuberculosis H37Rv EMBL AFN51052.1

Taxonomic identifier

83332 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Mycobacteriaceae › Mycobacterium › Mycobacterium tuberculosis complex ›

Protein attributes

Sequence length	507 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair By similarity. HAMAP-Rule MF_00407
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m). RuleBase RU000617 HAMAP-Rule MF_00407
Cofactor	Divalent metal cations By similarity. HAMAP-Rule MF_00407
Sequence similarities	Belongs to the ATP-dependent DNA ligase family. RuleBase RU004196 HAMAP-Rule MF_00407

Ontologies

Keywords
Biological process	Cell cycle Cell division HAMAP-Rule MF_00407 DNA damage DNA recombination RuleBase RU000617 HAMAP-Rule MF_00407 DNA repair RuleBase RU000617 HAMAP-Rule MF_00407 DNA replication RuleBase RU000617 HAMAP-Rule MF_00407
Ligand	ATP-binding RuleBase RU000617 HAMAP-Rule MF_00407 Metal-binding HAMAP-Rule MF_00407 Nucleotide-binding
Molecular function	Ligase RuleBase RU000617 HAMAP-Rule MF_00407 EMBL AFN51052.1
Gene Ontology (GO)
Biological_process	DNA ligation involved in DNA repair Inferred from electronic annotation. Source: InterPro DNA recombination Inferred from electronic annotation. Source: HAMAP DNA replication Inferred from electronic annotation. Source: HAMAP cell cycle Inferred from electronic annotation. Source: UniProtKB-KW cell division Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (ATP) activity Inferred from electronic annotation. Source: HAMAP metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Sites

Active site

211

1

N6-AMP-lysine intermediate By similarity HAMAP-Rule MF_00407

Binding site

209

1

ATP By similarity HAMAP-Rule MF_00407

Binding site

216

1

ATP By similarity HAMAP-Rule MF_00407

Binding site

231

1

ATP By similarity HAMAP-Rule MF_00407

Binding site

260

1

ATP By similarity HAMAP-Rule MF_00407

Binding site

300

1

ATP By similarity HAMAP-Rule MF_00407

Binding site

372

1

ATP By similarity HAMAP-Rule MF_00407

Binding site

378

1

ATP By similarity HAMAP-Rule MF_00407

Sequences

Sequence

Length

Mass (Da)

Tools

I6YB16 [UniParc].

Last modified October 3, 2012. Version 1.
Checksum: A382F41A7B9E5741
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FASTA

507

53,737

        10         20         30         40         50         60 
MLLHDVAITS MDVAATSSRL TKVARIAALL HRAAPDTQLV TIIVSWLSGE LPQRHIGVGW 

        70         80         90        100        110        120 
AALRSLPPPA PQPALTVTGV DATLSKIGTL PGKGSQAQRA ALVAELFSAA TEAEQTFLLR 

       130        140        150        160        170        180 
LLGGELRQGA KGGIMADAVA QAAGLPAATV QRAAMLGGDL AAAAAAGLSG AALDTFTLRV 

       190        200        210        220        230        240 
GRPIGPMLAQ TATSVHDALE RHGGTTIFEA KLDGARVQIH RANDQVRIYT RSLDDVTARL 

       250        260        270        280        290        300 
PEVVEATLAL PVRDLVADGE AIALCPDNRP QRFQVTASRF GRSVDVAAAR ATQPLSVFFF 

       310        320        330        340        350        360 
DILHRDGTDL LEAPTTERLA ALDALVPARH RVDRLITSDP TDAANFLDAT LAAGHEGVMA 

       370        380        390        400        410        420 
KAPAARYLAG RRGAGWLKVK PVHTLDLVVL AVEWGSGRRR GKLSNIHLGA RDPATGGFVM 

       430        440        450        460        470        480 
VGKTFKGMTD AMLDWQTTRF HEIAVGPTDG YVVQLRPEQV VEVALDGVQR SSRYPGGLAL 

       490        500 
RFARVVRYRA DKDPAEADTI DAVRALY

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References

[1]

"The Genome Sequence of Mycobacterium tuberculosis H37Rv."
The Broad Institute Genome Sequencing Platform, The Broad Institute Genome Sequencing Center for Infectious Disease
Galagan J., Walker B., Young S.K., Zeng Q., Gargeya S., Fitzgerald M., Haas B., Abouelleil A., Alvarado L., Arachchi H.M., Berlin A.M., Chapman S.B., Goldberg J., Griggs A., Gujja S., Hansen M., Howarth C., Imamovic A.

Birren B.
Submitted (JUL-2012) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE.
Strain: H37Rv EMBL AFN51052.1.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP003248 Genomic DNA. Translation: AFN51052.1.
RefSeq	NP_217578.1. NC_000962.3. YP_006516523.1. NC_018143.1.
3D structure databases
ProteinModelPortal	I6YB16.
SMR	I6YB16. Positions 76-507.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AFN51052; AFN51052; RVBD_3062.
GeneID	13317866. 887553.
KEGG	mtu:Rv3062. mtv:RVBD_3062.
Phylogenomic databases
KO	K01971.
OMA	ARVQVHK.
Family and domain databases
Gene3D	1.10.3260.10. 1 hit. 2.40.50.140. 1 hit.
HAMAP	MF_00407. DNA_ligase.
InterPro	IPR022865. DNA_ligae_ATP-dep_bac/arc. IPR000977. DNA_ligase_ATP-dep. IPR012309. DNA_ligase_ATP-dep_C. IPR012310. DNA_ligase_ATP-dep_cent. IPR016059. DNA_ligase_ATP-dep_CS. IPR012308. DNA_ligase_ATP-dep_N. IPR012340. NA-bd_OB-fold. [Graphical view]
Pfam	PF04679. DNA_ligase_A_C. 1 hit. PF01068. DNA_ligase_A_M. 1 hit. PF04675. DNA_ligase_A_N. 1 hit. [Graphical view]
SUPFAM	SSF50249. Nucleic_acid_OB. 1 hit. SSF117018. SSF117018. 1 hit.
TIGRFAMs	TIGR00574. dnl1. 1 hit.
PROSITE	PS00697. DNA_LIGASE_A1. 1 hit. PS50160. DNA_LIGASE_A3. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

I6YB16_MYCTU

Accession

Primary (citable) accession number: I6YB16

Entry history

Integrated into UniProtKB/TrEMBL:	October 3, 2012
Last sequence update:	October 3, 2012
Last modified:	May 1, 2013
This is version 8 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Family and domain databases

Entry information