1tae

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:28, 23 August 2023) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1tae.gif|left|200px]]
 
-
{{Structure
+
==Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal==
-
|PDB= 1tae |SIZE=350|CAPTION= <scene name='initialview01'>1tae</scene>, resolution 2.70&Aring;
+
<StructureSection load='1tae' size='340' side='right'caption='[[1tae]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> and <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>
+
<table><tr><td colspan='2'>[[1tae]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecalis_V583 Enterococcus faecalis V583]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TAE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TAE 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]] 2.7&#8491;</td></tr>
-
|GENE= ligA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226185 Enterococcus faecalis V583])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
}}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tae FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tae OCA], [https://pdbe.org/1tae PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tae RCSB], [https://www.ebi.ac.uk/pdbsum/1tae PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tae ProSAT]</span></td></tr>
-
 
+
</table>
-
'''Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/DNLJ_ENTFA DNLJ_ENTFA] 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 ==
-
==Overview==
+
[[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/ta/1tae_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=1tae ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
DNA ligase is an enzyme important for DNA repair and replication. Eukaryotic genomes encode ligases requiring ATP as the cofactor; bacterial genomes encode NAD(+)-dependent ligase. This difference in substrate specificities and the essentiality of NAD(+)-dependent ligase for bacterial survival make NAD(+)-dependent ligase a good target for designing highly specific anti-infectives. Any such structure-guided effort would require the knowledge of the precise mechanism of NAD+ recognition by the enzyme. We report the principles of NAD+ recognition by presenting the synthesis of NAD+ from nicotinamide mononucleotide (NMN) and AMP, catalyzed by Enterococcus faecalis ligase within the crystal lattice. Unprecedented conformational change, required to reorient the two subdomains of the protein for the condensation to occur and to recognize NAD+, is captured in two structures obtained using the same protein crystal. Structural data and sequence analysis presented here confirms and extends prior functional studies of the ligase adenylation reaction.
DNA ligase is an enzyme important for DNA repair and replication. Eukaryotic genomes encode ligases requiring ATP as the cofactor; bacterial genomes encode NAD(+)-dependent ligase. This difference in substrate specificities and the essentiality of NAD(+)-dependent ligase for bacterial survival make NAD(+)-dependent ligase a good target for designing highly specific anti-infectives. Any such structure-guided effort would require the knowledge of the precise mechanism of NAD+ recognition by the enzyme. We report the principles of NAD+ recognition by presenting the synthesis of NAD+ from nicotinamide mononucleotide (NMN) and AMP, catalyzed by Enterococcus faecalis ligase within the crystal lattice. Unprecedented conformational change, required to reorient the two subdomains of the protein for the condensation to occur and to recognize NAD+, is captured in two structures obtained using the same protein crystal. Structural data and sequence analysis presented here confirms and extends prior functional studies of the ligase adenylation reaction.
-
==About this Structure==
+
Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal.,Gajiwala KS, Pinko C Structure. 2004 Aug;12(8):1449-59. PMID:15296738<ref>PMID:15296738</ref>
-
1TAE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecalis_v583 Enterococcus faecalis v583]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TAE OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal., Gajiwala KS, Pinko C, Structure. 2004 Aug;12(8):1449-59. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15296738 15296738]
+
</div>
-
[[Category: DNA ligase (NAD(+))]]
+
<div class="pdbe-citations 1tae" style="background-color:#fffaf0;"></div>
-
[[Category: Enterococcus faecalis v583]]
+
-
[[Category: Single protein]]
+
-
[[Category: Gajiwala, K S.]]
+
-
[[Category: Pinko, C.]]
+
-
[[Category: NA]]
+
-
[[Category: NAD]]
+
-
[[Category: SO4]]
+
-
[[Category: nucleotidyl transferase fold]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:16:01 2008''
+
==See Also==
 +
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Enterococcus faecalis V583]]
 +
[[Category: Large Structures]]
 +
[[Category: Gajiwala KS]]
 +
[[Category: Pinko C]]

Current revision

Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal

PDB ID 1tae

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1tae"
Personal tools