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(-) Description

Title :  STRUCTURE OF ADENYLATION DOMAIN OF HAEMOPHILUS INFLUENZAE DNA LIGASES BOUND TO NAD+ IN ADENYLATED STATE.
 
Authors :  S. D. Lahiri
Date :  19 Nov 11  (Deposition) - 25 Jan 12  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Adenylated Protein, Atp-Grasp, Rossmann Fold, Adenylation, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. D. Lahiri, R. F. Gu, N. Gao, I. Karantzeni, G. K. Walkup, S. D. Mills
Structure Guided Understanding Of Nad(+) Recognition In Bacterial Dna Ligases.
Acs Chem. Biol. V. 7 571 2012
PubMed-ID: 22230472  |  Reference-DOI: 10.1021/CB200392G

(-) 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, UNP RESIDUES 3-324
    Gene: LIGA, LIG, LIGN, HI_1100
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 71421
    Strain: ATCC 51907 / DSM 11121 / KW20 / RD
    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
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:18 , TYR A:22 , PRO A:28 , VAL A:30 , PRO A:31 , ASP A:32 , TYR A:35 , ASP A:36 , PHE A:39 , HIS A:40 , LYS A:43 , ARG A:154 , HOH A:358 , HOH A:398 , HOH A:432 , HOH A:561 , HOH A:563 , HOH A:564 , HOH A:569 , HOH A:571 , HOH A:579BINDING SITE FOR RESIDUE NAD A 1
2AC2SOFTWAREHOH A:2 , LEU A:82 , GLU A:114 , LYS A:116 , GLY A:119 , ALA A:121 , ARG A:137 , GLU A:174 , ARG A:201 , TYR A:226 , VAL A:289 , LYS A:291 , LEU A:324 , HOH A:330 , HOH A:341 , HOH A:404 , HOH A:566 , HOH A:573BINDING SITE FOR RESIDUE AMP A 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UQ8)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:107 -Pro A:108

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UQ8)

(-) 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 3UQ8)

(-) 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:322
 aligned with DNLJ_HAEIN | P43813 from UniProtKB/Swiss-Prot  Length:670

    Alignment length:322
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322  
           DNLJ_HAEIN     3 NIQTQLDNLRKTLRQYEYEYHVLDNPSVPDSEYDRLFHQLKALELEHPEFLTSDSPTQRVGAKPLSGFSQIRHEIPMLSLDNAFSDAEFNAFVKRIEDRLILLPKPLTFCCEPKLDGLAVSILYVNGELTQAATRGDGTTGEDITANIRTIRNVPLQLLTDNPPARLEVRGEVFMPHAGFERLNKYALEHNEKTFANPRNAAAGSLRQLDPNITSKRPLVLNAYGIGIAEGVDLPTTHYARLQWLKSIGIPVNPEIRLCNGADEVLGFYRDIQNKRSSLGYDIDGTVLKINDIALQNELGFISKAPRWAIAYKFPAQEELTL 324
               SCOP domains d3uq8a_ A: automated matches                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhh..........eee.........ee.hhhhhhhhhhhhhhhh.......eeeeeeee..eeeeeeee..eeeeeee.....eee.hhhhhhh...............eeeeeeeee.hhhhhhhhhhhhhhh......hhhhhhhhhhh..hhhhhh....eeeeeeeeeee......hhhhhhhhhhhh........eeeehhhhhhhhhhhhhhh.......eeeeeeee.hhhhhhhhhee..ee..eeeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------DNA_LIGASE_N1  PDB: A:116-145 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uq8 A   3 NIQTQLDNLRKTLRQYEYEYHVLDNPSVPDSEYDRLFHQLKALELEHPEFLTSDSPTQRVGAKPLSGFSQIRHEIPMLSLDNAFSDAEFNAFVARIEDRLILLPAPLTFCCEPKLDGLAVSILYVNGELTQAATRGDGTTGEDITANIRTIRNVPLQLLTDNPPARLEVRGEVFMPHAGFERLNKYALEHNEKTFANPRNAAAGSLRQLDPNITSKRPLVLNAYGIGIAEGVDLPTTHYARLQWLKSIGIPVNPEIRLCNGADEVLGFYRDIQNKRSSLGYDIDGTVLKINDIALQNELGFISKAPRWAIAYKFPAQEELTL 324
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322
   Legend:   → Mismatch (orange background)
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  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 3UQ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UQ8)

(-) 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 3pn1 4uco 4ucr 4ucs 4uct 4ucu 4ucv 4ufz

(-) Related Entries Specified in the PDB File

3pn1 NOVEL BACTERIAL NAD+-DEPENDENT DNA LIGASE INHIBITORS WITH BROAD SPECTRUM POTENCY AND ANTIBACTERIAL EFFICACY IN VIVO