1yl5

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:58, 23 August 2023) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1yl5.png|left|200px]]
 
-
{{STRUCTURE_1yl5| PDB=1yl5 | SCENE= }}
+
==Crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (RV2773C) (crystal form A)==
 +
<StructureSection load='1yl5' size='340' side='right'caption='[[1yl5]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1yl5]] is a 2 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=1YL5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YL5 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]] 2.3&#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></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=1yl5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yl5 OCA], [https://pdbe.org/1yl5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yl5 RCSB], [https://www.ebi.ac.uk/pdbsum/1yl5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yl5 ProSAT], [https://www.topsan.org/Proteins/XMTB/1yl5 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/1yl5_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=1yl5 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.
-
===Crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (RV2773C) (crystal form A)===
+
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>
-
{{ABSTRACT_PUBMED_20057050}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 1yl5" style="background-color:#fffaf0;"></div>
-
[[1yl5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YL5 OCA].
+
== References ==
-
 
+
<references/>
-
==Reference==
+
__TOC__
-
<ref group="xtra">PMID:020057050</ref><references group="xtra"/>
+
</StructureSection>
-
[[Category: Dihydrodipicolinate reductase]]
+
[[Category: Large Structures]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Mycobacterium tuberculosis]]
-
[[Category: Janowski, R.]]
+
[[Category: Janowski R]]
-
[[Category: Kefala, G.]]
+
[[Category: Kefala G]]
-
[[Category: TBSGC, TB Structural Genomics Consortium.]]
+
[[Category: Weiss MS]]
-
[[Category: Weiss, M S.]]
+
-
[[Category: Dihydrodipicolinate]]
+
-
[[Category: Lysine biosynthesis]]
+
-
[[Category: Nadh]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Protein structure initiative]]
+
-
[[Category: Psi]]
+
-
[[Category: Reductase]]
+
-
[[Category: Structural genomic]]
+
-
[[Category: Tb structural genomics consortium]]
+
-
[[Category: Tbsgc]]
+

Current revision

Crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (RV2773C) (crystal form A)

PDB ID 1yl5

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/1yl5"
Personal tools