3flu: Difference between revisions

Latest revision as of 15:30, 1 November 2023

Crystal structure of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis

Structural highlights

3flu is a 4 chain structure with sequence from Neisseria meningitidis serogroup B. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	GOL, SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DAPA_NEIMB Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).^[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

Neisseria meningitidis is an obligate commensal bacterium of humans, and also an important human pathogen. To facilitate future drug studies, we report here the biochemical and structural characterisation of a key enzyme in (S)-lysine biosynthesis, dihydrodipicolinate synthase (DHDPS), from N. meningitidis (NmeDHDPS). X-ray crystallography revealed only minor structural differences between NmeDHDPS and the enzyme from E. coli at the active and allosteric effector sites. The catalytic capabilities of NmeDHDPS are similar to those of the enzyme from E. coli, but intriguingly NmeDHDPS is subject to substrate inhibition by high concentrations of the second substrate, (S)-aspartate semialdehyde, and is also significantly more sensitive to feedback inhibition by (S)-lysine. This heightened sensitivity to inhibition at both active and allosteric sites suggests that it may be possible to target DHDPS from N. meningitidis for antibiotic development.

Cloning and characterisation of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis.,Devenish SR, Huisman FH, Parker EJ, Hadfield AT, Gerrard JA Biochim Biophys Acta. 2009 Aug;1794(8):1168-74. Epub 2009 Feb 21. PMID:19236959^[2]

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

References

↑ Devenish SR, Huisman FH, Parker EJ, Hadfield AT, Gerrard JA. Cloning and characterisation of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis. Biochim Biophys Acta. 2009 Aug;1794(8):1168-74. Epub 2009 Feb 21. PMID:19236959 doi:10.1016/j.bbapap.2009.02.003
↑ Devenish SR, Huisman FH, Parker EJ, Hadfield AT, Gerrard JA. Cloning and characterisation of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis. Biochim Biophys Acta. 2009 Aug;1794(8):1168-74. Epub 2009 Feb 21. PMID:19236959 doi:10.1016/j.bbapap.2009.02.003

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Devenish SR, Huisman FH, Parker EJ, Hadfield AT, Gerrard JA. Cloning and characterisation of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis. Biochim Biophys Acta. 2009 Aug;1794(8):1168-74. Epub 2009 Feb 21. PMID:19236959 doi:10.1016/j.bbapap.2009.02.003

[2] Devenish SR, Huisman FH, Parker EJ, Hadfield AT, Gerrard JA. Cloning and characterisation of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis. Biochim Biophys Acta. 2009 Aug;1794(8):1168-74. Epub 2009 Feb 21. PMID:19236959 doi:10.1016/j.bbapap.2009.02.003

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='3flu' size='340' side='right'caption='[[3flu]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3flu]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Neimi Neimi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FLU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FLU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3flu]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_meningitidis_serogroup_B Neisseria meningitidis serogroup B]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FLU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FLU FirstGlance]. <br>
-</td></tr><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=SO4:SULFATE+ION'>SO4</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&#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;'>[[1yxc|1yxc]], [[1yxd|1yxd]]</div></td></tr>
+<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=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapA, NMB0929 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=491 NEIMI])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_synthase 4-hydroxy-tetrahydrodipicolinate synthase], with EC number [https://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=3flu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3flu OCA], [https://pdbe.org/3flu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3flu RCSB], [https://www.ebi.ac.uk/pdbsum/3flu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3flu ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/DAPA_NEIMB DAPA_NEIMB]] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).<ref>PMID:19236959</ref>
+[https://www.uniprot.org/uniprot/DAPA_NEIMB DAPA_NEIMB] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).<ref>PMID:19236959</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 38: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: 4-hydroxy-tetrahydrodipicolinate synthase]]
 [[Category: Large Structures]]
-[[Category: Neimi]]
+[[Category: Neisseria meningitidis serogroup B]]
-[[Category: Devenish, S R.A]]
+[[Category: Devenish SRA]]
-[[Category: Hadfield, A T]]
+[[Category: Hadfield AT]]
-[[Category: Amino-acid biosynthesis]]
-[[Category: Beta-alpha-barrel]]
-[[Category: Diaminopimelate biosynthesis]]
-[[Category: Lyase]]
-[[Category: Lysine biosynthesis]]
-[[Category: Schiff base]]
-[[Category: Tim barrel]]

3flu: Difference between revisions

Latest revision as of 15:30, 1 November 2023

Crystal structure of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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