5ees: Difference between revisions
New page: ==Crystal strcuture of DapB in complex with NADP+ from Corynebacterium glutamicum== <StructureSection load='5ees' size='340' side='right' caption='5ees, resolution 2.15... |
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==Crystal | ==Crystal structure of DapB in complex with NADP+ from Corynebacterium glutamicum== | ||
<StructureSection load='5ees' size='340' side='right' caption='[[5ees]], [[Resolution|resolution]] 2.15Å' scene=''> | <StructureSection load='5ees' size='340' side='right'caption='[[5ees]], [[Resolution|resolution]] 2.15Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5ees]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EES OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5ees]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum_ATCC_13032 Corynebacterium glutamicum ATCC 13032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EES OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EES FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=5ees FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ees OCA], [https://pdbe.org/5ees PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ees RCSB], [https://www.ebi.ac.uk/pdbsum/5ees PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ees ProSAT]</span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/DAPB_CORGL DAPB_CORGL] Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate.[HAMAP-Rule:MF_00102] | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Corynebacterium glutamicum ATCC 13032]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Kim K-J]] | ||
[[Category: | [[Category: Sagong H-Y]] | ||
Latest revision as of 09:23, 5 July 2023
Crystal structure of DapB in complex with NADP+ from Corynebacterium glutamicumCrystal structure of DapB in complex with NADP+ from Corynebacterium glutamicum
Structural highlights
FunctionDAPB_CORGL Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate.[HAMAP-Rule:MF_00102] Publication Abstract from PubMedDihydrodipicolinate reductase is an enzyme that converts dihydrodipicolinate to tetrahydrodipicolinate using an NAD(P)H cofactor in L-lysine biosynthesis. To increase the understanding of the molecular mechanisms of lysine biosynthesis, we determined the crystal structure of dihydrodipicolinate reductase from Corynebacterium glutamicum (CgDapB). CgDapB functions as a tetramer, and each protomer is composed of two domains, an Nterminal domain and a C-terminal domain. The N-terminal domain mainly contributes to nucleotide binding, whereas the C-terminal domain is involved in substrate binding. We elucidated the mode of cofactor binding to CgDapB by determining the crystal structure of the enzyme in complex with NADP(+) and found that CgDapB utilizes both NADH and NADPH as cofactors. Moreover, we determined the substrate binding mode of the enzyme based on the coordination mode of two sulfate ions in our structure. Compared with Mycobacterium tuberculosis DapB in complex with its cofactor and inhibitor, we propose that the domain movement for active site constitution occurs when both cofactor and substrate bind to the enzyme. Structural Insight into Dihydrodipicolinate Reductase from Corybebacterium glutamicum for Lysine Biosynthesis.,Sagong HY, Kim KJ J Microbiol Biotechnol. 2016 Feb;26(2):226-32. doi: 10.4014/jmb.1508.08086. PMID:26502738[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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