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(-) Description

Title :  STRUCTURAL BASIS FOR THE INHIBITION OF BACTERIAL NAD+ DEPENDENT DNA LIGASE
 
Authors :  C. Pinko
Date :  07 Nov 07  (Deposition) - 11 Nov 08  (Release) - 13 Jul 11  (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

(-) 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
    Organism Common: STREPTOCOCCUS FAECALIS
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
13BA1Ligand/Ion7-AMINO-2-TERT-BUTYL-4-{[2-(1H-IMIDAZOL-4-YL)ETHYL]AMINO}PYRIDO[2,3-D]PYRIMIDINE-6-CARBOXAMIDE
2GOL2Ligand/IonGLYCEROL
3NMN1Ligand/IonBETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
4SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:120 , GLU A:175 , 3BA A:501 , HOH A:802 , HOH A:840BINDING SITE FOR RESIDUE SO4 A 402
2AC2SOFTWAREPRO A:81 , ARG A:129 , ARG A:137 , HOH A:647 , HOH A:832BINDING SITE FOR RESIDUE SO4 A 403
3AC3SOFTWAREARG A:190 , GLN A:195 , GLN A:211 , ARG A:220 , HOH A:792 , HOH A:863BINDING SITE FOR RESIDUE SO4 A 404
4AC4SOFTWAREGLN A:24 , HIS A:27 , LYS A:32BINDING SITE FOR RESIDUE SO4 A 405
5AC5SOFTWARETYR 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:622 , HOH A:658 , HOH A:703 , HOH A:734 , HOH A:785BINDING SITE FOR RESIDUE NMN A 401
6AC6SOFTWARETYR A:87 , LEU A:89 , GLU A:118 , LEU A:119 , LYS A:120 , ILE A:121 , GLU A:175 , TYR A:227 , VAL A:289 , LYS A:291 , TRP A:310 , SO4 A:402 , GOL A:603BINDING SITE FOR RESIDUE 3BA A 501
7AC7SOFTWAREPHE A:101 , ARG A:104 , ARG A:309 , HOH A:684 , HOH A:806BINDING SITE FOR RESIDUE GOL A 602
8AC8SOFTWAREPRO A:85 , MET A:86 , TYR A:87 , ARG A:173 , PHE A:303 , 3BA A:501 , HOH A:872BINDING SITE FOR RESIDUE GOL A 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_LIGASE_N1PS01055 NAD-dependent DNA ligase signature 1.DNLJ_ENTFA120-149  1A:120-149

(-) Exons   (0, 0)

(no "Exon" information available for 3BAA)

(-) 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:312
 aligned with DNLJ_ENTFA | Q837V6 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:312
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315  
           DNLJ_ENTFA     6 LTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDERVRKAIGKPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLTEPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKAPRWAIAYKFP 317
               SCOP domains d3baaa_ A: Adenylation domain of NAD+-dependent DNA ligase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3baaA01 A:6-68 Helix hairpin bin                               -------------------3baaA02 A:88-122,A:254-317         -3baaA03 A:124-253 DNA ligase/mRNA capping enzyme                                                                                  3baaA02 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......hhhhhhhhhh...hhhhhh....eeeeeee.........hhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhh........eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------DNA_LIGASE_N1  PDB: A:120-149 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3baa A   6 LTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDERVRKAIGKPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLTEPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKAPRWAIAYKFP 317
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

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.

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 Related Entries

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UniProtKB/Swiss-Prot
        DNLJ_ENTFA | Q837V6: 1ta8 1tae 3ba8 3ba9 3bab 4eeq 4efb 4efe 4lh6 4lh7

(-) Related Entries Specified in the PDB File

3ba8 3ba9 3bab