1yl7: Difference between revisions

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[[Image:1yl7.gif|left|200px]]<br /><applet load="1yl7" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1yl7, resolution 2.34&Aring;" />
'''the crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) in complex with NADH (crystal form C)'''<br />


==About this Structure==
==the crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) in complex with NADH (crystal form C)==
1YL7 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=NAD:'>NAD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Dihydrodipicolinate_reductase Dihydrodipicolinate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.26 1.3.1.26] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YL7 OCA].  
<StructureSection load='1yl7' size='340' side='right'caption='[[1yl7]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
[[Category: Dihydrodipicolinate reductase]]
== Structural highlights ==
<table><tr><td colspan='2'>[[1yl7]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YL7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YL7 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.34&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</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=1yl7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yl7 OCA], [https://pdbe.org/1yl7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yl7 RCSB], [https://www.ebi.ac.uk/pdbsum/1yl7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yl7 ProSAT], [https://www.topsan.org/Proteins/TBSGC/1yl7 TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DAPB_MYCTU DAPB_MYCTU] Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate (Probable). Can use both NADH and NADPH as a reductant, with NADH being 6-fold as effective as NADPH.<ref>PMID:12962488</ref>
== 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/yl/1yl7_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=1yl7 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Dihydrodipicolinate reductase (DHDPR, DapB) is an enzyme that belongs to the L-lysine biosynthetic pathway. DHDPR reduces the alpha,beta-unsaturated cyclic imine 2,3-dihydrodipicolinic acid to yield the compound 2,3,4,5-tetrahydrodipicolinic acid in a pyridine nucleotide-dependent reaction. The substrate of this reaction is the unstable product of the preceding enzyme dihydrodipicolinate synthase (DHDPS, DapA). Here, the structure of apo-DHDPR from Mycobacterium tuberculosis is reported in two orthorhombic crystal forms, as well as the structure of DHDPR from M. tuberculosis in complex with NADH in a monoclinic crystal form. A comparison of the results with previously solved structures of this enzyme shows that DHDPR undergoes a major conformational change upon binding of its cofactor. This conformational change can be interpreted as one of the low-frequency normal modes of the structure.
 
The structure of dihydrodipicolinate reductase (DapB) from Mycobacterium tuberculosis in three crystal forms.,Janowski R, Kefala G, Weiss MS Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):61-72. Epub 2009, Dec 21. PMID:20057050<ref>PMID:20057050</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1yl7" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Single protein]]
[[Category: Janowski R]]
[[Category: Janowski, R.]]
[[Category: Kefala G]]
[[Category: Kefala, G.]]
[[Category: Weiss MS]]
[[Category: TBSGC, TB Structural Genomics Consortium.]]
[[Category: Weiss, M S.]]
[[Category: MG]]
[[Category: NAD]]
[[Category: dihydrodipicolinate]]
[[Category: lysine biosynthesis]]
[[Category: nadh]]
[[Category: protein structure initiative]]
[[Category: psi]]
[[Category: reductase]]
[[Category: structural genomics]]
[[Category: tb structural genomics consortium]]
[[Category: tbsgc]]
 
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Retrieved from "https://proteopedia.org/1yl7"