DB code: T00254

CATH domain	3.30.1490.70 : Dna Ligase; domain 1	Catalytic domain
	2.40.50.140 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Catalytic domain
	3.30.470.30 : D-amino Acid Aminotransferase; Chain A, domain 1
E.C.	6.5.1.1
CSA	1a0i
M-CSA	1a0i
MACiE	M0202

CATH domain	Related DB codes (homologues)
2.40.50.140 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)	M00220 M00186 T00050 D00291 D00294

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	RefSeq	Pfam
P00969	DNA ligase	EC 6.5.1.1 Polydeoxyribonucleotide synthase [ATP]	NP_041963.1 (Protein) NC_001604.1 (DNA/RNA sequence)	PF01068 (DNA_ligase_A_M) [Graphical View]
O41026		A544R protein	NP_048900.1 (Protein) NC_000852.5 (DNA/RNA sequence)	PF01068 (DNA_ligase_A_M) [Graphical View]

KEGG enzyme name
deoxyribonucleic acid-joining enzyme deoxyribonucleic repair enzyme deoxyribonucleic joinase deoxyribonucleic acid ligase deoxyribonucleic acid joinase deoxyribonucleic acid repair enzyme DNA ligase (ATP) polydeoxyribonucleotide synthase (ATP) polynucleotide ligase sealase DNA repair enzyme DNA joinase DNA ligase deoxyribonucleic ligase deoxyribonucleate ligase DNA-joining enzyme deoxyribonucleic-joining enzyme

KEGG enzyme name

deoxyribonucleic acid-joining enzyme
deoxyribonucleic repair enzyme
deoxyribonucleic joinase
deoxyribonucleic acid ligase
deoxyribonucleic acid joinase
deoxyribonucleic acid repair enzyme
DNA ligase (ATP)
polydeoxyribonucleotide synthase (ATP)
polynucleotide ligase
sealase
DNA repair enzyme
DNA joinase
DNA ligase
deoxyribonucleic ligase
deoxyribonucleate ligase
DNA-joining enzyme
deoxyribonucleic-joining enzyme

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
P00969	DNLI_BPT7	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).
O41026	O41026_PBCV1

KEGG Pathways
Map code	Pathways	E.C.

Compound table
	Cofactors	Substrates					Products				Intermediates
KEGG-id	C00305	C00002	C00039	C00039	C00046	C00046	C00020	C00013	C00039	C00046
E.C.
Compound	Magnesium	ATP	(Deoxyribonucleotide)n	(Deoxyribonucleotide)m	(Ribonucleotide)n	(Ribonucleotide)m	AMP	Pyrophosphate	(Deoxyribonucleotide)n+m	(Ribonucleotide)n+m
Type	divalent metal (Ca2+, Mg2+)	amine group,nucleotide	nucleic acids	nucleic acids	nucleic acids	nucleic acids	amine group,nucleotide	phosphate group/phosphate ion	nucleic acids	nucleic acids
ChEBI	18420 18420	15422 15422					16027 16027	29888 29888
PubChem	888 888	5957 5957					6083 6083	1023 21961011 1023 21961011

1a0iA01	Unbound	Bound:ATP	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1fviA01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Intermediate-bound:AMP (bound to Lys27)
1a0iA02	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1fviA02	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1a0iA03	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1fviA03	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Analogue:SO4	Unbound	Unbound	Unbound

Reference for Active-site residues
resource	references	E.C.
PDB;1a0i & literature [1], [7] & [8]

Active-site residues
PDB	Catalytic residues	Cofactor-binding residues	Modified residues	Main-chain involved in catalysis	Comment

1a0iA01	LYS 34;LYS 238	ASP 36(divalent metal binding)			mutant M2V
1fviA01	LYS 27;LYS 186				mutant D29A
1a0iA02	LYS 240
1fviA02	LYS 188
1a0iA03
1fviA03

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[1]	p.608, p.611-612
[2]	Fig.1	3
[7]	p.47, p.51-52, Fig.10	5
[8]

References
[1]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS)
Medline ID	96222302
PubMed ID	8653795
Journal	Cell
Year	1996
Volume	85
Pages	607-15
Authors	Subramanya HS, Doherty AJ, Ashford SR, Wigley DB
Title	Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7.
Related PDB	1a0i
Related UniProtKB	P00969
[2]
Resource
Comments
Medline ID
PubMed ID	8626651
Journal	J Biol Chem
Year	1996
Volume	271
Pages	11083-9
Authors	Doherty AJ, Ashford SR, Subramanya HS, Wigley DB
Title	Bacteriophage T7 DNA ligase. Overexpression, purification, crystallization, and characterization.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID	8646532
Journal	Nat Struct Biol
Year	1996
Volume	3
Pages	496
Authors	Riddihough G
Title	DNA ligase shows restraint.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID	9254695
Journal	Nucleic Acids Res
Year	1997
Volume	25
Pages	3403-7
Authors	Pritchard CE, Southern EM
Title	Effects of base mismatches on joining of short oligodeoxynucleotides by DNA ligases.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID	9016621
Journal	Nucleic Acids Res
Year	1997
Volume	25
Pages	727-34
Authors	Sekiguchi J, Shuman S
Title	Domain structure of vaccinia DNA ligase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID	9878388
Journal	J Mol Biol
Year	1999
Volume	285
Pages	63-71
Authors	Doherty AJ, Wigley DB
Title	Functional domains of an ATP-dependent DNA ligase.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID	10656817
Journal	J Mol Biol
Year	2000
Volume	296
Pages	43-56
Authors	Doherty AJ, Dafforn TR
Title	Nick recognition by DNA ligases.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID	11106756
Journal	Mol Cell
Year	2000
Volume	6
Pages	1183-93
Authors	Odell M, Sriskanda V, Shuman S, Nikolov DB
Title	Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining.
Related PDB	1fvi
Related UniProtKB

Comments

Created	Updated
2004-03-25	2009-02-26