4ns3: Difference between revisions

Revision as of 08:36, 18 January 2023

Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis bound with NAD and cobalamin

Structural highlights

4ns3 is a 6 chain structure with sequence from Mycobacterium tuberculosis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	B12, CME, NAD
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

O50443_MYCTU

Publication Abstract from PubMed

The use of small molecules as "silver bullets" that can bind to generate crosslinks between protein molecules has been advanced as a powerful means of enhancing success in protein crystallization (McPherson and Cudney, 2006). We have explored this approach in attempts to overcome an order-disorder phenomenon that complicated the structural analysis of the enzyme Delta1-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis (P5CDH, Mtb-PruA). Using the Silver Bullets Bio screen, we obtained new crystal packing using cobalamin as a co-crystallization agent. This crystal form did not display the order-disorder phenomenon previously encountered. Solution of the crystal structure showed that cobalamin molecules are present in the crystal contacts. Although the cobalamin binding probably does not have physiological relevance, it reflects similarities in the nucleotide-binding region of Mtb-PruA, with the nucleotide loop of cobalamin sharing the binding site for the adenine moiety of NAD+.

Use of a "silver bullet" to resolve crystal lattice dislocation disorder: A cobalamin complex of Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis.,Lagautriere T, Bashiri G, Baker EN J Struct Biol. 2014 Dec 31. pii: S1047-8477(14)00281-0. doi:, 10.1016/j.jsb.2014.12.007. PMID:25557497^[1]

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

References

↑ Lagautriere T, Bashiri G, Baker EN. Use of a "silver bullet" to resolve crystal lattice dislocation disorder: A cobalamin complex of Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis. J Struct Biol. 2014 Dec 31. pii: S1047-8477(14)00281-0. doi:, 10.1016/j.jsb.2014.12.007. PMID:25557497 doi:https://dx.doi.org/10.1016/j.jsb.2014.12.007

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OCA

[1] Lagautriere T, Bashiri G, Baker EN. Use of a "silver bullet" to resolve crystal lattice dislocation disorder: A cobalamin complex of Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis. J Struct Biol. 2014 Dec 31. pii: S1047-8477(14)00281-0. doi:, 10.1016/j.jsb.2014.12.007. PMID:25557497 doi:https://dx.doi.org/10.1016/j.jsb.2014.12.007

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='4ns3' size='340' side='right'caption='[[4ns3]], [[Resolution|resolution]] 2.38&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ns3]] is a 6 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=4NS3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NS3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ns3]] is a 6 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=4NS3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NS3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</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=4ns3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ns3 OCA], [https://pdbe.org/4ns3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ns3 RCSB], [https://www.ebi.ac.uk/pdbsum/4ns3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ns3 ProSAT]</span></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4lem|4lem]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MT1224, pruA, rocA, Rv1187 ([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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-pyrroline-5-carboxylate_dehydrogenase 1-pyrroline-5-carboxylate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.12 1.5.1.12] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ns3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ns3 OCA], [http://pdbe.org/4ns3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ns3 RCSB], [http://www.ebi.ac.uk/pdbsum/4ns3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ns3 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/O50443_MYCTU O50443_MYCTU]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 27: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: 1-pyrroline-5-carboxylate dehydrogenase]]
 [[Category: Large Structures]]
-[[Category: Baker, E N]]
+[[Category: Mycobacterium tuberculosis]]
-[[Category: Bashiri, G]]
+[[Category: Baker EN]]
-[[Category: Lagautriere, T]]
+[[Category: Bashiri G]]
-[[Category: Dehydrogenase]]
+[[Category: Lagautriere T]]
-[[Category: Dehydrogenation]]
-[[Category: Oxidoreductase]]
-[[Category: Rossmann fold]]

4ns3: Difference between revisions

Revision as of 08:36, 18 January 2023

Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis bound with NAD and cobalamin

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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