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(-) Description

Title :  STRUCTURE OF THE ADENYLATION DOMAIN OF AN NAD+ DEPENDENT LIGASE
 
Authors :  M. R. Singleton, K. Hakansson, D. J. Timson, D. B. Wigley
Date :  16 Nov 98  (Deposition) - 22 Nov 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ligase, Dna Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Singleton, K. Hakansson, D. J. Timson, D. B. Wigley
Structure Of The Adenylation Domain Of An Nad+-Dependent Dna Ligase.
Structure Fold. Des. V. 7 35 1999
PubMed-ID: 10368271  |  Reference-DOI: 10.1016/S0969-2126(99)80007-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (DNA LIGASE)
    Chains: A, B
    EC Number: 6.5.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Gene: LIG
    Expression System Plasmid: PET21D
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: ADENYLATION DOMAIN
    Gene: LIG
    Mutation: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Strain: NCA 1503

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1B04)

(-) Sites  (0, 0)

(no "Site" information available for 1B04)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B04)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1B04)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B04)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_LIGASE_N1PS01055 NAD-dependent DNA ligase signature 1.DNLJ_GEOSE114-143
 		  2A:115-143
B:115-143
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_LIGASE_N1PS01055 NAD-dependent DNA ligase signature 1.DNLJ_GEOSE114-143
 		  1A:115-143
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_LIGASE_N1PS01055 NAD-dependent DNA ligase signature 1.DNLJ_GEOSE114-143
 		  1-
B:115-143

(-) Exons   (0, 0)

(no "Exon" information available for 1B04)

(-) Sequences/Alignments

Asymmetric 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:310
 aligned with DNLJ_GEOSE | O87703 from UniProtKB/Swiss-Prot  Length:670

    Alignment length:312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311  
           DNLJ_GEOSE     2 DRQQAERRAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIAIEEQYPELKTSDSPTQRIGGPPLEAFRKVAHRVPMMSLANAFGEGDLRDFDRRVRQEVGEAAYVCELKIDGLAVSVRYEDGYFVQGATRGDGTTGEDITENLKTIRSLPLRLKEPVSLEARGEAFMPKASFLRLNEERKARGEELFANPRNAAAGSLRQLDPKVAASRQLDLFVYGLADAEALGIASHSEALDYLQALGFKVNPERRRCANIDEVIAFVSEWHDKRPQLPYEIDGIVIKVDSFAQQRALGATAKSPRWAIAYKFPAE 313
               SCOP domains d1b04a_ A: Adenylation domain of NAD+-dependent DNA ligase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1b04A03 A:2-63 Helix hairpin bin                              -------------------1b04A02 A:83-116,A:248-312        -1b04A01 A:118-247 DNA ligase/mRNA capping enzyme                                                                                  1b04A02 A:83-116,A:248-312  [code=3.30.1490.70, no name defined] - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.hhh.....hhhh............................hhhhhhhhhhhhh....eeeeeee..eeeeeeee..eeeeeee..........hhhhhh.............eeeeeeeee.hhhhhhhhhhhhh.--.....hhhhhhhhhh...hhhhhhh.eeeeeeee..........hhhhhhhhhhh........eee..hhhhhhhhhhhhhh.......eeeeeeee..hhhhhhh.........eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------DNA_LIGASE_N1  PDB: A:115-143 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1b04 A   2 DRQQAERRAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIAIEEQYPELKTSDSPTQRIGGPPLEAFRKVAHRVPMMSLANAFGEGDLRDFDRRVRQEVGEAAYVCELAIDGLAVSVRYEDGYFVQGATRGDGTTGEDITENLKTIRSLPLRLKEPVSLEARGEAFMPKASFLRLNEERKAR--ELFANPRNAAAGSLRQLDPKVAASRQLDLFVYGLADAEALGIASHSEALDYLQALGFKVNPERRRCANIDEVIAFVSEWHDKRPQLPYEIDGIVIKVDSFAQQRALGATAKSPRWAIAYKFPAE 313
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181     | 191       201       211       221       231       241       251       261       271       281       291       301       311  
                                                                                                                                                                                                                   187  |                                                                                                                           
                                                                                                                                                                                                                      190                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:311
 aligned with DNLJ_GEOSE | O87703 from UniProtKB/Swiss-Prot  Length:670

    Alignment length:313
                                    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_GEOSE     1 MDRQQAERRAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIAIEEQYPELKTSDSPTQRIGGPPLEAFRKVAHRVPMMSLANAFGEGDLRDFDRRVRQEVGEAAYVCELKIDGLAVSVRYEDGYFVQGATRGDGTTGEDITENLKTIRSLPLRLKEPVSLEARGEAFMPKASFLRLNEERKARGEELFANPRNAAAGSLRQLDPKVAASRQLDLFVYGLADAEALGIASHSEALDYLQALGFKVNPERRRCANIDEVIAFVSEWHDKRPQLPYEIDGIVIKVDSFAQQRALGATAKSPRWAIAYKFPAE 313
               SCOP domains d1b04b_ B: Adenylation domain of NAD+-dependent DNA ligase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains -1b04B03 B:2-63 Helix hairpin bin                              -------------------1b04B02 B:83-116,B:248-312        -1b04B01 B:118-247 DNA ligase/mRNA capping enzyme                                                                                  1b04B02 B:83-116,B:248-312  [code=3.30.1490.70, no name defined] - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.hhh.....hhhhh.........................hhhhhhhhhhhhhhh....eeeeeee..eeeeeeee..eeeeeee..........hhhhhh.............eeeeeeeee.hhhhhhhhhhhhhh--.....hhhhhhhhhh...hhhhhh..eeeeeeee..........hhhhhhhhhhh........eee..hhhhhhhhhhhhhhhhh....eeeeeeee..hhhhhhh.........eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------DNA_LIGASE_N1  PDB: B:115-143 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b04 B   1 MDRQQAERRAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIAIEEQYPELKTSDSPTQRIGGPPLEAFRKVAHRVPMMSLANAFGEGDLRDFDRRVRQEVGEAAYVCELAIDGLAVSVRYEDGYFVQGATRGDGTTGEDITENLKTIRSLPLRLKEPVSLEARGEAFMPKASFLRLNEERKAR--ELFANPRNAAAGSLRQLDPKVAASRQLDLFVYGLADAEALGIASHSEALDYLQALGFKVNPERRRCANIDEVIAFVSEWHDKRPQLPYEIDGIVIKVDSFAQQRALGATAKSPRWAIAYKFPAE 313
                                    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   
                                                                                                                                                                                                                    187  |                                                                                                                           
                                                                                                                                                                                                                       190
   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, 2)

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

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B04)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DNLJ_GEOSE | O87703)
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: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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