1yl6: Difference between revisions

Latest revision as of 06:58, 23 August 2023

crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) (crystal form B)

Structural highlights

1yl6 is a 2 chain structure with sequence from Mycobacterium tuberculosis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:	MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

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.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Cirilli M, Zheng R, Scapin G, Blanchard JS. The three-dimensional structures of the Mycobacterium tuberculosis dihydrodipicolinate reductase-NADH-2,6-PDC and -NADPH-2,6-PDC complexes. Structural and mutagenic analysis of relaxed nucleotide specificity. Biochemistry. 2003 Sep 16;42(36):10644-50. PMID:12962488 doi:https://dx.doi.org/10.1021/bi030044v
↑ Janowski R, Kefala G, Weiss MS. The structure of dihydrodipicolinate reductase (DapB) from Mycobacterium tuberculosis in three crystal forms. Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):61-72. Epub 2009, Dec 21. PMID:20057050 doi:10.1107/S0907444909043960

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OCA

[1] Cirilli M, Zheng R, Scapin G, Blanchard JS. The three-dimensional structures of the Mycobacterium tuberculosis dihydrodipicolinate reductase-NADH-2,6-PDC and -NADPH-2,6-PDC complexes. Structural and mutagenic analysis of relaxed nucleotide specificity. Biochemistry. 2003 Sep 16;42(36):10644-50. PMID:12962488 doi:https://dx.doi.org/10.1021/bi030044v

[2] Janowski R, Kefala G, Weiss MS. The structure of dihydrodipicolinate reductase (DapB) from Mycobacterium tuberculosis in three crystal forms. Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):61-72. Epub 2009, Dec 21. PMID:20057050 doi:10.1107/S0907444909043960

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='1yl6' size='340' side='right'caption='[[1yl6]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1yl6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YL6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1YL6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1yl6]] 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=1YL6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YL6 FirstGlance]. <br>
-</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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1yl5|1yl5]], [[1yl7|1yl7]]</div></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=1yl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yl6 OCA], [https://pdbe.org/1yl6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yl6 RCSB], [https://www.ebi.ac.uk/pdbsum/1yl6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yl6 ProSAT], [https://www.topsan.org/Proteins/XMTB/1yl6 TOPSAN]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_reductase 4-hydroxy-tetrahydrodipicolinate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.1.8 1.17.1.8] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1yl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yl6 OCA], [http://pdbe.org/1yl6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yl6 RCSB], [http://www.ebi.ac.uk/pdbsum/1yl6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yl6 ProSAT], [http://www.topsan.org/Proteins/XMTB/1yl6 TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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]]
@@ Line 35: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: 4-hydroxy-tetrahydrodipicolinate reductase]]
 [[Category: Large Structures]]
-[[Category: Janowski, R]]
+[[Category: Mycobacterium tuberculosis]]
-[[Category: Kefala, G]]
+[[Category: Janowski R]]
-[[Category: Structural genomic]]
+[[Category: Kefala G]]
-[[Category: Weiss, M S]]
+[[Category: Weiss MS]]
-[[Category: Dihydrodipicolinate]]
-[[Category: Lysine biosynthesis]]
-[[Category: Nadh]]
-[[Category: Oxidoreductase]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Reductase]]
-[[Category: Tbsgc]]

1yl6: Difference between revisions

Latest revision as of 06:58, 23 August 2023

crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) (crystal form B)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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