1b04: Difference between revisions

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[[Image:1b04.gif|left|200px]]


{{Structure
==STRUCTURE OF THE ADENYLATION DOMAIN OF AN NAD+ DEPENDENT LIGASE==
|PDB= 1b04 |SIZE=350|CAPTION= <scene name='initialview01'>1b04</scene>, resolution 2.8&Aring;
<StructureSection load='1b04' size='340' side='right'caption='[[1b04]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<table><tr><td colspan='2'>[[1b04]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B04 FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/DNA_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
|GENE= LIG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b04 OCA], [https://pdbe.org/1b04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b04 RCSB], [https://www.ebi.ac.uk/pdbsum/1b04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b04 ProSAT]</span></td></tr>
}}
</table>
== Function ==
[https://www.uniprot.org/uniprot/DNLJ_GEOSE DNLJ_GEOSE] DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA (By similarity).
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b0/1b04_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1b04 ConSurf].
<div style="clear:both"></div>


'''STRUCTURE OF THE ADENYLATION DOMAIN OF AN NAD+ DEPENDENT LIGASE'''
==See Also==
 
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
BACKGROUND: DNA ligases catalyse phosphodiester bond formation between adjacent bases in nicked DNA, thereby sealing the nick. A key step in the catalytic mechanism is the formation of an adenylated DNA intermediate. The adenyl group is derived from either ATP (in eucaryotes and archaea) or NAD+4 (in bacteria). This difference in cofactor specificity suggests that DNA ligase may be a useful antibiotic target. RESULTS: The crystal structure of the adenylation domain of the NAD+-dependent DNA ligase from Bacillus stearothermophilus has been determined at 2.8 A resolution. Despite a complete lack of detectable sequence similarity, the fold of the central core of this domain shares homology with the equivalent region of ATP-dependent DNA ligases, providing strong evidence for the location of the NAD+-binding site. CONCLUSIONS: Comparison of the structure of the NAD+4-dependent DNA ligase with that of ATP-dependent ligases and mRNA-capping enzymes demonstrates the manifold utilisation of a conserved nucleotidyltransferase domain within this family of enzymes. Whilst this conserved core domain retains a common mode of nucleotide binding and activation, it is the additional domains at the N terminus and/or the C terminus that provide the alternative specificities and functionalities in the different members of this enzyme superfamily.
 
==About this Structure==
1B04 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B04 OCA].
 
==Reference==
Structure of the adenylation domain of an NAD+-dependent DNA ligase., Singleton MR, Hakansson K, Timson DJ, Wigley DB, Structure. 1999 Jan 15;7(1):35-42. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10368271 10368271]
[[Category: DNA ligase (NAD(+))]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Hakansson, K.]]
[[Category: Hakansson K]]
[[Category: Singleton, M R.]]
[[Category: Singleton MR]]
[[Category: Timson, D J.]]
[[Category: Timson DJ]]
[[Category: Wigley, D B.]]
[[Category: Wigley DB]]
[[Category: dna replication]]
[[Category: ligase]]
 
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Retrieved from "https://proteopedia.org/1b04"