DNA ligase - Brucella melitensis

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Reviewed, UniProtKB/Swiss-Prot Q8YI56 (DNLJ_BRUME)

Last modified November 3, 2009. Version 55. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    DNA ligase
    EC=6.5.1.2
Alternative name(s):
    Polydeoxyribonucleotide synthase [NAD+]

Gene names

Name:	ligA
Ordered Locus Names:	BMEI0589

Organism

Brucella melitensis [Complete proteome] [HAMAP]

Taxonomic identifier

29459 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Brucellaceae › Brucella

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Protein attributes

Sequence length	719 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Inferred from homology.

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General annotation (Comments)

Function	DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA By similarity.
Catalytic activity	NAD⁺ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + nicotinamide nucleotide + (deoxyribonucleotide)(n+m). HAMAP MF_01588
Cofactor	Magnesium or manganese By similarity.
Sequence similarities	Belongs to the NAD-dependent DNA ligase family. LigA subfamily. Contains 1 BRCT domain.

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Ontologies

Keywords
Biological process	DNA damage DNA repair DNA replication
Ligand	Magnesium Manganese Metal-binding NAD Zinc
Molecular function	Ligase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW DNA replication Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	intracellular Inferred from electronic annotation. Source: InterPro
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (NAD+) activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 719

719

DNA ligase HAMAP MF_01588

PRO_0000313154

Regions

Domain

640 – 719

BRCT

Nucleotide binding

42 – 46

NAD By similarity

Nucleotide binding

92 – 93

NAD By similarity

Sites

Active site

128

N6-AMP-lysine intermediate By similarity

Metal binding

430

Zinc By similarity

Metal binding

433

Zinc By similarity

Metal binding

448

Zinc By similarity

Metal binding

454

Zinc By similarity

Binding site

126

NAD By similarity

Binding site

149

NAD By similarity

Binding site

185

NAD By similarity

Binding site

301

NAD By similarity

Binding site

325

NAD By similarity

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Sequences

Sequence

Length

Mass (Da)

Tools

Q8YI56-1 [UniParc].

Last modified March 1, 2002. Version 1.
Checksum: 74FB18F1E16CB9B8
Show »

FASTA

719

78,692

        10         20         30         40         50         60 
MSDISVEKLT ELEAAAELER LARAIAHHDE LYHAKDRPEI SDAAYDALKR RNEAIEAHFP 

        70         80         90        100        110        120 
ALVRDDSPSR RVGAAPALAI FAPVVHARPM LSLDNAFSDE DVRDFVGSVY RFLGQLPDDS 

       130        140        150        160        170        180 
IAFTAEPKID GLSMSIRYEN GILVSGATRG DGTTGENVTA NIRTIAEIPN RLPAGAPAVV 

       190        200        210        220        230        240 
EVRGEVYMAK SDFLTLNAQM EAEGKQTYVN PRNTAAGSLR QLDAKVTASR KLRFFAYAWG 

       250        260        270        280        290        300 
EMSDMPADTQ LGMVEVFRQW GFPVNPLMKR FNSVDGLLAH YRAIGMERPT LDYDIDGVVY 

       310        320        330        340        350        360 
KVDRLDLQTR LGFRSRSPRW AIAHKFPAEQ ALTILRGIDI QVGRTGALTP VARLEPITVG 

       370        380        390        400        410        420 
GVVVTNATLH NEDYIKGIGQ KGEPIREGRD IRIGDSVIVQ RAGDVIPQIV DVVLEEGKKR 

       430        440        450        460        470        480 
GEPYQFPHVC PACGSHAVRE EGEAVRRCTG GLICPAQAVE RIRHFVSRNA FDIEGLGEKQ 

       490        500        510        520        530        540 
VEFFFNAEDP ALCIRSPADI FTLKKRQENS LTKLQNIEGF GATSVKKLYD AIDARREIAL 

       550        560        570        580        590        600 
HRFLFGLGIR HVGEVNAKRL ARAYLSYAAF KKAALEAVPP KEGDRTDKGS EAWQDMLAVE 

       610        620        630        640        650        660 
GIGSIVAEAV VDFYGEPHNR EVLAALLAEV TPLDEEARVA TGSPVEGKTV VFTGSLERMS 

       670        680        690        700        710 
RDEAKAMAER HGAKTAGSVS KKTDLVVAGP GAGSKLAKAT ELGIEVINED DWFKLVGED

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References

[1]

"The genome sequence of the facultative intracellular pathogen Brucella melitensis."
DelVecchio V.G., Kapatral V., Redkar R.J., Patra G., Mujer C., Los T., Ivanova N., Anderson I., Bhattacharyya A., Lykidis A., Reznik G., Jablonski L., Larsen N., D'Souza M., Bernal A., Mazur M., Goltsman E., Selkov E.

Overbeek R.
Proc. Natl. Acad. Sci. U.S.A. 99:443-448(2002) [PubMed: 11756688] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: 16M / ATCC 23456 / NCTC 10094 / Biotype 1.

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Cross-references

Sequence databases
	AE008917 Genomic DNA. Translation: AAL51770.1.
PIR	AG3325.
RefSeq	NP_539506.1.
3D structure databases
HSSP	HSSP built from PDB template 1B04 based on UniProtKB O87703.
ModBase	Search...
Genome annotation databases
GeneID	1196300.
GenomeReviews	Gene locus BMEI0589 in contig AE008917_GR.
KEGG	bme:BMEI0589.
NMPDR	fig\|224914.1.peg.588.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q8YI56.
OMA	YKFPAQE.
Enzyme and pathway databases
BioCyc	BMEL224914:BMEI0589-MON.
BRENDA	6.5.1.2. 277959.
Family and domain databases
HAMAP	MF_01588. [Tree]
InterPro	IPR001357. BRCT. IPR018239. DNA_ligase_AS. IPR004150. DNA_ligase_OB. IPR001679. DNAligase. IPR013839. DNAligase_adenylation. IPR013840. DNAligase_N. IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif. IPR012340. NA-bd_OB-fold. IPR004149. Znf_DNAligase_C4. [Graphical view]
Gene3D	G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.
Pfam	PF00533. BRCT. 1 hit. PF01653. DNA_ligase_aden. 1 hit. PF03120. DNA_ligase_OB. 1 hit. PF03119. DNA_ligase_ZBD. 1 hit. [Graphical view]
PIRSF	PIRSF001604. LigA. 1 hit.
ProDom	PD003944. DNAligase. 1 hit. [Graphical view] [Entries sharing at least one domain]
SMART	SM00292. BRCT. 1 hit. SM00278. HhH1. 2 hits. SM00532. LIGANc. 1 hit. [Graphical view]
TIGRFAMs	TIGR00575. dnlj. 1 hit.
PROSITE	PS50172. BRCT. 1 hit. PS01055. DNA_LIGASE_N1. 1 hit. PS01056. DNA_LIGASE_N2. 1 hit. [Graphical view]
ProtoNet	Search...

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Entry information

Entry name

DNLJ_BRUME

Accession

Primary (citable) accession number: Q8YI56

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	March 1, 2002
Last modified:	November 3, 2009
This is version 55 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

Brucella melitensis

Brucella melitensis (strain 16M): entries and gene names

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents