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(-) Description

Title :  NOVEL BACTERIAL NAD+-DEPENDENT DNA LIGASE INHIBITORS WITH BROAD SPECTRUM POTENCY AND ANTIBACTERIAL EFFICACY IN VIVO
 
Authors :  S. Mills, A. Eakin, E. Buurman, J. Newman, N. Gao, H. Huynh, K. Johnson, S A. Shapiro, G. Walkup, Y. Wei, S. Stokes
Date :  18 Nov 10  (Deposition) - 12 Jan 11  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Atp Grasp Fold, Ligase, Dna, Bacteria, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. D. Mills, A. E. Eakin, E. T. Buurman, J. V. Newman, N. Gao, H. Huynh, K. D. Johnson, S. Lahiri, A. B. Shapiro, G. K. Walkup, W. Yang, S. S. Stokes
Novel Bacterial Nad+-Dependent Dna Ligase Inhibitors With Broad-Spectrum Activity And Antibacterial Efficacy In Vivo.
Antimicrob. Agents Chemother. V. 55 1088 2011
PubMed-ID: 21189350  |  Reference-DOI: 10.1128/AAC.01181-10

(-) Compounds

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, LIG, LIGN, HI_1100
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Synonym: POLYDEOXYRIBONUCLEOTIDE SYNTHASE [NAD+]

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1IVH1Ligand/Ion2-(BUTYLSULFANYL)ADENOSINE
2IWH1Ligand/Ion1-(2,4-DIMETHYLBENZYL)-6-OXO-1,6-DIHYDROPYRIDINE-3-CARBOXAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:82 , GLU A:114 , PRO A:115 , LYS A:116 , LEU A:117 , ALA A:121 , ARG A:137 , GLU A:174 , TYR A:226 , VAL A:289 , LYS A:291 , HOH A:397 , HOH A:534BINDING SITE FOR RESIDUE IVH A 319
2AC2SOFTWARETYR A:18 , TYR A:22 , HIS A:23 , ASN A:27 , VAL A:30 , PRO A:31 , ASP A:32 , TYR A:35 , HOH A:329 , HOH A:346BINDING SITE FOR RESIDUE IWH A 320

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PN1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PN1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PN1)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_LIGASE_N1PS01055 NAD-dependent DNA ligase signature 1.DNLJ_HAEIN116-145  1A:116-145

(-) Exons   (0, 0)

(no "Exon" information available for 3PN1)

(-) Sequences/Alignments

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:318
 aligned with DNLJ_HAEIN | P43813 from UniProtKB/Swiss-Prot  Length:670

    Alignment length:318
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310        
           DNLJ_HAEIN     1 MTNIQTQLDNLRKTLRQYEYEYHVLDNPSVPDSEYDRLFHQLKALELEHPEFLTSDSPTQRVGAKPLSGFSQIRHEIPMLSLDNAFSDAEFNAFVKRIEDRLILLPKPLTFCCEPKLDGLAVSILYVNGELTQAATRGDGTTGEDITANIRTIRNVPLQLLTDNPPARLEVRGEVFMPHAGFERLNKYALEHNEKTFANPRNAAAGSLRQLDPNITSKRPLVLNAYGIGIAEGVDLPTTHYARLQWLKSIGIPVNPEIRLCNGADEVLGFYRDIQNKRSSLGYDIDGTVLKINDIALQNELGFISKAPRWAIAYKFPA 318
               SCOP domains d3pn1a_ A: automated matches                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -DNA_ligase_aden-3pn1A01 A:2-318                                                                                                                                                                                                                                                                                               Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhh..........eee.........ee.hhhhhhhhhhhhhhhh.......eeeeeeee..eeeeeeee..eeeeeee.....eee.hhhhhhh...............eeeeeeeee.hhhhhhhhhhhhhh.......hhhhhhhhhhh..hhhhhh....eeeeeeeeeee......hhhhhhhhhhhh........eeeehhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhee..ee..eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------DNA_LIGASE_N1  PDB: A:116-145 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pn1 A   1 MTNIQTQLDNLRKTLRQYEYEYHVLDNPSVPDSEYDRLFHQLKALELEHPEFLTSDSPTQRVGAKPLSGFSQIRHEIPMLSLDNAFSDAEFNAFVKRIEDRLILLPKPLTFCCEPKLDGLAVSILYVNGELTQAATRGDGTTGEDITANIRTIRNVPLQLLTDNPPARLEVRGEVFMPHAGFERLNKYALEHNEKTFANPRNAAAGSLRQLDPNITSKRPLVLNAYGIGIAEGVDLPTTHYARLQWLKSIGIPVNPEIRLCNGADEVLGFYRDIQNKRSSLGYDIDGTVLKINDIALQNELGFISKAPRWAIAYKFPA 318
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
   Legend:   → Mismatch (orange background)
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  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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PN1)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: DNA_ligase (17)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DNLJ_HAEIN | P43813)
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: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:0006288    base-excision repair, DNA ligation    The ligation by DNA ligase of DNA strands. Ligation occurs after polymerase action to fill the gap left by the action of endonucleases during base-excision repair.
    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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DNLJ_HAEIN | P43813: 3bac 3uq8 4uco 4ucr 4ucs 4uct 4ucu 4ucv 4ufz

(-) Related Entries Specified in the PDB File

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