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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURAL BASIS FOR THE INHIBITION OF BACTERIAL NAD+ DEPENDENT DNA LIGASE

Authors :   C. Pinko

Date :   07 Nov 07 (Deposition) - 11 Nov 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Adenylation Domain, Dna Damage, Dna Repair, Dna Replication, Ligase, Nad (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Pinko, A. Borchardt, V. Nikulin, Y. Su
Structural Basis For The Inhibition Of Bacterial Nad+ Dependent Dna Ligase
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - DNA LIGASE
	Chains	:	A
	EC Number	:	6.5.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	ADENYLATION DOMAIN
	Gene	:	LIGA
	Organism Common	:	STREPTOCOCCUS FAECALIS
	Organism Scientific	:	ENTEROCOCCUS FAECALIS
	Organism Taxid	:	1351

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	3B8	1	Ligand/Ion	2-AMINO-7-FLUORO-5-OXO-5H-CHROMENO[2,3-B]PYRIDINE-3-CARBOXAMIDE
2	NMN	1	Ligand/Ion	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:124 , ALA A:125 , ARG A:141 , HOH A:527 , HOH A:560 , HOH A:567 , HOH A:641	BINDING SITE FOR RESIDUE SO4 A 402
2	AC2	SOFTWARE	PRO A:81 , ARG A:129 , ARG A:137 , HOH A:522 , HOH A:695 , HOH A:733	BINDING SITE FOR RESIDUE SO4 A 403
3	AC3	SOFTWARE	ARG A:190 , GLN A:195 , GLN A:211 , ARG A:220 , HOH A:556	BINDING SITE FOR RESIDUE SO4 A 404
4	AC4	SOFTWARE	TYR A:25 , TYR A:29 , TYR A:30 , VAL A:37 , ASP A:39 , TYR A:42 , ASP A:43 , ARG A:158 , HOH A:507 , HOH A:593 , HOH A:612	BINDING SITE FOR RESIDUE NMN A 401
5	AC5	SOFTWARE	TYR A:87 , LEU A:89 , GLU A:118 , LEU A:119 , LYS A:120 , ILE A:121 , ARG A:141 , GLU A:175 , TYR A:227 , LYS A:291 , PRO A:308 , TRP A:310	BINDING SITE FOR RESIDUE 3B8 A 501

(no "SS Bond" information available for 3BA8)

(no "Cis Peptide Bond" information available for 3BA8)

(no "SAP(SNP)/Variant" information available for 3BA8)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_LIGASE_N1	PS01055	NAD-dependent DNA ligase signature 1.	DNLJ_ENTFA	120-149	1	A:120-149

(no "Exon" information available for 3BA8)

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:313
 aligned with DNLJ_ENTFA | Q837V6 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:313
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314   
           DNLJ_ENTFA     5 PLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDERVRKAIGKPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLTEPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKAPRWAIAYKFP 317
               SCOP domains d3ba8a_ A: Adenylation domain of NAD+-dependent DNA ligase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 3ba8A01 A:5-68 Helix hairpin bin                                -------------------3ba8A02 A:88-122,A:254-317         -3ba8A03 A:124-253 DNA ligase/mRNA capping enzyme                                                                                  3ba8A02 A:88-122,A:254-317  [code=3.30.1490.70, no name defined] CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh........eee.........ee.hhhhhhhhhhhhhhhhh....eeeeeee..eeeeeeee..eeeeeee.....eee.hhhhhh..............eeeeeeee.hhhhhhhhhhhhhhh......hhhhhhhhhhh..hhhhhhhh..eeeeeeeee.......hhhhhhhhhhhh........eee.hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhh........eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------DNA_LIGASE_N1  PDB: A:120-149 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ba8 A   5 PLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDERVRKAIGKPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLTEPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKAPRWAIAYKFP 317
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314

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)

Enterococcus faecalis [TaxId: 1351] (9)

d3ba8a_

(no "Pfam Domain" information available for 3BA8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DNLJ_ENTFA | Q837V6)

molecular function
	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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ba8)

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	DNLJ_ENTFA \| Q837V6	:	1ta8 1tae 3ba9 3baa 3bab 4eeq 4efb 4efe 4lh6 4lh7

Description

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Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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