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Title :   CRYSTAL STRUCTURE OF THE ADENYLATION DOMAIN OF NAD+-DEPENDENT DNA LIGASE FROM STAPHYLOCOCCUS AUREUS

Authors :   S. Han, J. S. Chang, M. Griffor

Date :   10 Sep 09 (Deposition) - 15 Dec 09 (Release) - 15 Dec 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Dna Ligase, Nad+-Dependent, Staphylococcus Aureus, Dna Damage, Dna Repair, Dna Replication, Ligase, Magnesium, Manganese, Metal-Binding, Nad, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Han, J. S. Chang, M. Griffor
Structure Of The Adenylation Domain Of Nad(+)-Dependent Dna Ligase From Staphylococcus Aureus.
Acta Crystallogr. , Sect. F V. 65 1078 2009
PubMed-ID: 19923722 | Reference-DOI: 10.1107/S1744309109036872
(for further references see the PDB file header)

Molecule 1 - DNA LIGASE
	Chains	:	A, B
	EC Number	:	6.5.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	ADENYLATION DOMAIN (UNP RESIDUES 1-312)
	Gene	:	LIGA
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Synonym	:	POLYDEOXYRIBONUCLEOTIDE SYNTHASE [NAD+]

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 8)

No.	Name	Count	Type	Full Name
1	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:115 , LEU A:116 , ALA A:117 , ARG A:133 , ARG A:194 , HOH A:441 , HOH A:444	BINDING SITE FOR RESIDUE SO4 A 402
2	AC2	SOFTWARE	MET A:79 , LEU A:80 , ARG A:165 , TYR A:219 , SER A:220 , HOH A:511 , HOH A:518	BINDING SITE FOR RESIDUE SO4 A 404
3	AC3	SOFTWARE	ALA A:2 , HIS A:49 , HOH A:485 , HOH A:536 , ASN B:74 , HOH B:387 , HOH B:423	BINDING SITE FOR RESIDUE SO4 A 406
4	AC4	SOFTWARE	ASN A:74 , HOH A:448 , HOH A:499 , HOH A:508 , ALA B:2 , HIS B:49	BINDING SITE FOR RESIDUE SO4 A 407
5	AC5	SOFTWARE	LYS A:182 , PHE A:190 , ARG A:212 , LYS A:241	BINDING SITE FOR RESIDUE SO4 A 408
6	AC6	SOFTWARE	GLY B:115 , LEU B:116 , ALA B:117 , ARG B:133 , ARG B:194 , HOH B:458 , HOH B:464	BINDING SITE FOR RESIDUE SO4 B 403
7	AC7	SOFTWARE	MET B:79 , LEU B:80 , ARG B:165 , TYR B:219 , HOH B:441 , HOH B:460 , HOH B:462	BINDING SITE FOR RESIDUE SO4 B 405
8	AC8	SOFTWARE	LYS B:182 , PHE B:190 , GLN B:203 , ARG B:212 , HOH B:452	BINDING SITE FOR RESIDUE SO4 B 409

(no "SS Bond" information available for 3JSL)

(no "Cis Peptide Bond" information available for 3JSL)

(no "SAP(SNP)/Variant" information available for 3JSL)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_LIGASE_N1	PS01055	NAD-dependent DNA ligase signature 1.	DNLJ_STAAU	112-141	2	A:112-141 B:112-141

(no "Exon" information available for 3JSL)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:308
 aligned with DNLJ_STAAU | Q9AIU7 from UniProtKB/Swiss-Prot  Length:667

    Alignment length:308
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301        
           DNLJ_STAAU     2 ADLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSLGNAFNEDDLRKFDQRIREQIGNVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKEPLNVEVRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNARSQSEALDELDKLGFTTNKNRARVNNIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFP 309
               SCOP domains d3jsla_ A: Adenylation domain of NAD+-dependent DNA ligase                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh........eee........eee.hhhhhhhhhhhhhhhh....eeeeeee..eeeeeeee..eeeeeee.....eee.hhhhhh..............eeeeeeee.hhhhhhhhhhhhh........hhhhhhhhhhh..hhhhhhhh..eeeeeee.........hhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhh........eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------DNA_LIGASE_N1  PDB: A:112-141 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jsl A   2 ADLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSLGNAFNEDDLRKFDQRIREQIGNVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKEPLNVEVRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNARSQSEALDELDKLGFTTNKNRARVNNIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFP 309
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301

Chain B from PDB  Type:PROTEIN  Length:308
 aligned with DNLJ_STAAU | Q9AIU7 from UniProtKB/Swiss-Prot  Length:667

    Alignment length:308
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301        
           DNLJ_STAAU     2 ADLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSLGNAFNEDDLRKFDQRIREQIGNVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKEPLNVEVRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNARSQSEALDELDKLGFTTNKNRARVNNIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFP 309
               SCOP domains d3jslb_ B: Adenylation domain of NAD+-dependent DNA ligase                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) DNA_ligase_aden-3jslB01 B:2-309                                                                                                                                                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) DNA_ligase_aden-3jslB02 B:2-309                                                                                                                                                                                                                                                                                      Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh........eee........eee.hhhhhhhhhhhhhhhh....eeeeeee..eeeeeeee..eeeeeee.....eee.hhhhhh..............eeeeeeee.hhhhhhhhhhhhhhh......hhhhhhhhhhh..hhhhhhhh..eeeeeee.........hhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhh........eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------DNA_LIGASE_N1  PDB: B:112-141 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jsl B   2 ADLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSLGNAFNEDDLRKFDQRIREQIGNVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKEPLNVEVRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNARSQSEALDELDKLGFTTNKNRARVNNIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFP 309
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: ATP-grasp (191)

Superfamily: DNA ligase/mRNA capping enzyme, catalytic domain (33)

Family: Adenylation domain of NAD+-dependent DNA ligase (16)

Protein domain: Adenylation domain of NAD+-dependent DNA ligase (14)

Staphylococcus aureus [TaxId: 1280] (2)

1a	d3jsla_	A:
1b	d3jslb_	B:

(no "CATH Domain" information available for 3JSL)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DNA_ligase (17)

Family: DNA_ligase_aden (7)

Staphylococcus aureus (2)

1a	DNA_ligase_aden-3jslB01	B:2-309
1b	DNA_ligase_aden-3jslB02	B:2-309

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DNLJ_STAAU | Q9AIU7)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003911	DNA ligase (NAD+) activity	Catalysis of the reaction: NAD+ + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + nicotinamide nucleotide + deoxyribonucleotide(n+m).
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006266	DNA ligation	The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.
	GO:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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