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(-) Description

Title :  LAST STOP ON THE ROAD TO REPAIR: STRUCTURE OF E.COLI DNA LIGASE BOUND TO NICKED DNA-ADENYLATE
 
Authors :  S. Shuman, J. Nandakumar, P. A. Nair
Date :  16 Feb 07  (Deposition) - 15 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dna, Ligase, Protein-Dna Complex, Ligase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Nandakumar, P. A. Nair, S. Shuman
Last Stop On The Road To Repair: Structure Of E. Coli Dna Ligase Bound To Nicked Dna-Adenylate.
Mol. Cell V. 26 257 2007
PubMed-ID: 17466627  |  Reference-DOI: 10.1016/J.MOLCEL.2007.02.026

(-) Compounds

Molecule 1 - 26-MER
    ChainsB
    EngineeredYES
    Other DetailsCHEMICALLY SYNTHESIZED
    SyntheticYES
 
Molecule 2 - 5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3'
    ChainsC
    EngineeredYES
    Other DetailsCHEMICALLY SYNTHESIZED
    SyntheticYES
 
Molecule 3 - 5'-D(*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*G)-3'
    ChainsD
    EngineeredYES
    Other DetailsCHEMICALLY SYNTHESIZED
    SyntheticYES
 
Molecule 4 - DNA LIGASE
    ChainsA
    EC Number6.5.1.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-LIGA
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePET16B
    GeneLIGA
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12
    SynonymPOLYDEOXYRIBONUCLEOTIDE SYNTHASE [NAD+]

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2OMC1Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
3SO44Ligand/IonSULFATE ION
4ZN1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:408 , CYS A:411 , CYS A:426 , CYS A:432BINDING SITE FOR RESIDUE ZN A 672
2AC2SOFTWAREARG A:446 , ARG A:447 , HOH A:922 , HOH C:42 , DC D:40BINDING SITE FOR RESIDUE SO4 A 673
3AC3SOFTWAREARG A:74 , ARG A:510 , HOH A:718 , HOH A:759BINDING SITE FOR RESIDUE SO4 A 674
4AC4SOFTWAREASN A:95 , GLN A:99 , SER A:262 , ALA A:263 , HOH A:799BINDING SITE FOR RESIDUE SO4 A 675
5AC5SOFTWAREHIS A:559 , ASN A:562BINDING SITE FOR RESIDUE SO4 A 676
6AC6SOFTWARESER A:81 , LEU A:82 , GLU A:113 , LYS A:115 , ALA A:120 , ARG A:136 , GLU A:173 , TYR A:225 , VAL A:288 , LYS A:290 , HOH A:752 , HOH C:137 , DC D:40BINDING SITE FOR RESIDUE AMP D 53

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OWO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OWO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OWO)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_LIGASE_N1PS01055 NAD-dependent DNA ligase signature 1.DNLJ_ECOLI115-144  1A:115-144
2DNA_LIGASE_N2PS01056 NAD-dependent DNA ligase signature 2.DNLJ_ECOLI331-346  1A:331-346

(-) Exons   (0, 0)

(no "Exon" information available for 2OWO)

(-) 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:586
 aligned with DNLJ_ECOLI | P15042 from UniProtKB/Swiss-Prot  Length:671

    Alignment length:586
                                    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       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580      
           DNLJ_ECOLI     1 MESIEQQLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHPELITPDSPTQRVGAAPLAAFSQIRHEVPMLSLDNVFDEESFLAFNKRVQDRLKNNEKVTWCCELKLDGLAVSILYENGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLHGENIPARLEVRGEVFLPQAGFEKINEDARRTGGKVFANPRNAAAGSLRQLDPRITAKRPLTFFCYGVGVLEGGELPDTHLGRLLQFKKWGLPVSDRVTLCESAEEVLAFYHKVEEDRPTLGFDIDGVVIKVNSLAQQEQLGFVARAPRWAVAFKFPAQEQMTFVRDVEFQVGRTGAITPVARLEPVHVAGVLVSNATLHNADEIERLGLRIGDKVVIRRAGDVIPQVVNVVLSERPEDTREVVFPTHCPVCGSDVERVEGEAVARCTGGLICGAQRKESLKHFVSRRAMDVDGMGDKIIDQLVEKEYVHTPADLFKLTAGKLTGLERMGPKSAQNVVNALEKAKETTFARFLYALGIREVGEATAAGLAAYFGTLEALEAASIEELQKVPDVGIVVASHVHNFFAEESNRNVISELLAEGVHWPAP 586
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -DNA_ligase_aden-2owoA01 A:2-318                                                                                                                                                                                                                                                                                              -DNA_ligase_OB-2owoA02 A:320-401                                                   -----DNA_ligase_ZBD-2owoA03      -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.......hhhhh..........eee........eee.hhhhhhhhhhhhhhhh.......eeeeeee..eeeeeeee..eeeeee......eee.hhhhhhh...............eeeeeeeee.hhhhhhhhhhhhhhh......hhhhhhhhhhh..hhhhhhh...eeeeeeeeeee......hhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhh........eeeee....eeeeeeeeeeeee.....eeeeeeeeeeee..eeeeeee..hhhhhhhhh.....eeeeeeehhheeeeeee.hhhh...................eee......eee.hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------DNA_LIGASE_N1  PDB: A:115-144 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_LIGASE_N2   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2owo A   1 MESIEQQLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHPELITPDSPTQRVGAAPLAAFSQIRHEVPMLSLDNVFDEESFLAFNKRVQDRLKNNEKVTWCCELKLDGLAVSILYENGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLHGENIPARLEVRGEVFLPQAGFEKINEDARRTGGKVFANPRNAAAGSLRQLDPRITAKRPLTFFCYGVGVLEGGELPDTHLGRLLQFKKWGLPVSDRVTLCESAEEVLAFYHKVEEDRPTLGFDIDGVVIKVNSLAQQEQLGFVARAPRWAVAFKFPAQEQMTFVRDVEFQVGRTGAITPVARLEPVHVAGVLVSNATLHNADEIERLGLRIGDKVVIRRAGDVIPQVVNVVLSERPEDTREVVFPTHCPVCGSDVERVEGEAVARCTGGLICGAQRKESLKHFVSRRAMDVDGMGDKIIDQLVEKEYVHTPADLFKLTAGKLTGLERMGPKSAQNVVNALEKAKETTFARFLYALGIREVGEATAAGLAAYFGTLEALEAASIEELQKVPDVGIVVASHVHNFFAEESNRNVISELLAEGVHWPAP 586
                                    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       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580      

Chain B from PDB  Type:DNA  Length:26
                                                          
                 2owo B   1 CATTCCGATAGTGGGGTCGCAATTGT  26
                                    10        20      

Chain C from PDB  Type:DNA/RNA  Length:13
                                             
                 2owo C  27 ACAATTGCGACcC  39
                                    36 | 
                                      38-OMC

Chain D from PDB  Type:DNA  Length:13
                                             
                 2owo D  40 CACTATCGGAATG  52
                                    49   

   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  (0, 0)

(no "SCOP Domain" information available for 2OWO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OWO)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: OB (224)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DNLJ_ECOLI | P15042)
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:0070403    NAD+ binding    Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
    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: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_ECOLI | P150424glx 5tt5

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