6tzu: Difference between revisions

Latest revision as of 07:41, 11 October 2023

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84A mutant with pyruvate bound in the active site

Structural highlights

6tzu is a 6 chain structure with sequence from Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	ACT, EDO, GOL, KPI, MG, PEG, PGE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DAPA_CAMJE Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).[HAMAP-Rule:MF_00418]

Publication Abstract from PubMed

Dihydrodipicolinate synthase (DHDPS) from Campylobacter jejuni is a natively homotetrameric enzyme that catalyzes the first unique reaction of (S)-lysine biosynthesis and is feedback-regulated by lysine through binding to an allosteric site. High-resolution structures of the DHDPS-lysine complex have revealed significant insights into the binding events. One key asparagine residue, N84, makes hydrogen bonds with both the carboxyl and the alpha-amino group of the bound lysine. We generated two mutants, N84A and N84D, to study the effects of these changes on the allosteric site properties. However, under normal assay conditions, N84A displayed notably lower catalytic activity, and N84D showed no activity. Here we show that these mutations disrupt the quaternary structure of DHDPS in a concentration-dependent fashion, as demonstrated by size-exclusion chromatography, multi-angle light scattering, dynamic light scattering, small-angle X-ray scattering (SAXS) and high-resolution protein crystallography.

Asparagine-84, a regulatory allosteric site residue, helps maintain the quaternary structure of Campylobacter jejuni dihydrodipicolinate synthase.,Majdi Yazdi M, Saran S, Mrozowich T, Lehnert C, Patel TR, Sanders DAR, Palmer DRJ J Struct Biol. 2019 Oct 31:107409. doi: 10.1016/j.jsb.2019.107409. PMID:31678256^[1]

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

References

↑ Majdi Yazdi M, Saran S, Mrozowich T, Lehnert C, Patel TR, Sanders DAR, Palmer DRJ. Asparagine-84, a regulatory allosteric site residue, helps maintain the quaternary structure of Campylobacter jejuni dihydrodipicolinate synthase. J Struct Biol. 2019 Oct 31:107409. doi: 10.1016/j.jsb.2019.107409. PMID:31678256 doi:https://dx.doi.org/10.1016/j.jsb.2019.107409

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OCA

[1] Majdi Yazdi M, Saran S, Mrozowich T, Lehnert C, Patel TR, Sanders DAR, Palmer DRJ. Asparagine-84, a regulatory allosteric site residue, helps maintain the quaternary structure of Campylobacter jejuni dihydrodipicolinate synthase. J Struct Biol. 2019 Oct 31:107409. doi: 10.1016/j.jsb.2019.107409. PMID:31678256 doi:https://dx.doi.org/10.1016/j.jsb.2019.107409

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='6tzu' size='340' side='right'caption='[[6tzu]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6tzu]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6TZU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6tzu]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Campylobacter_jejuni_subsp._jejuni_NCTC_11168_=_ATCC_700819 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TZU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 1.8&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KPI:(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC+ACID'>KPI</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KPI:(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC+ACID'>KPI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></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_synthase 4-hydroxy-tetrahydrodipicolinate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.3.7 4.3.3.7] </span></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=6tzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tzu OCA], [https://pdbe.org/6tzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tzu RCSB], [https://www.ebi.ac.uk/pdbsum/6tzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tzu ProSAT]</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=6tzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tzu OCA], [http://pdbe.org/6tzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tzu RCSB], [http://www.ebi.ac.uk/pdbsum/6tzu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tzu ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DAPA_CAMJE DAPA_CAMJE]] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).[HAMAP-Rule:MF_00418]
+[https://www.uniprot.org/uniprot/DAPA_CAMJE DAPA_CAMJE] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).[HAMAP-Rule:MF_00418]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 19: @@
 </div>
 <div class="pdbe-citations 6tzu" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Dihydrodipicolinate synthase|Dihydrodipicolinate synthase]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: 4-hydroxy-tetrahydrodipicolinate synthase]]
+[[Category: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819]]
 [[Category: Large Structures]]
-[[Category: Lehnert, C]]
+[[Category: Lehnert C]]
-[[Category: Palmer, D R.J]]
+[[Category: Majdi Yazdi M]]
-[[Category: Sanders, D A.R]]
+[[Category: Palmer DRJ]]
-[[Category: Saran, S]]
+[[Category: Sanders DAR]]
-[[Category: Yazdi, M Majdi]]
+[[Category: Saran S]]
-[[Category: Allostery]]
-[[Category: Campylobacter jejuni]]
-[[Category: Dihydrodipicolinate synthase]]
-[[Category: Lyase]]
-[[Category: Tetrameric protein]]
-[[Category: Tim barrel]]

6tzu: Difference between revisions

Latest revision as of 07:41, 11 October 2023

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84A mutant with pyruvate bound in the active site

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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