4eou: Difference between revisions

Revision as of 07:21, 28 September 2022

Crystal structure of E. coli dihydrodipicolinate synthase with pyruvate and succinic semi-aldehyde bound in active site

Structural highlights

4eou is a 2 chain structure with sequence from Escherichia coli. This structure supersedes the now removed PDB entry 3ubs. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	GOL, K, LYF
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DAPA_ECOLI] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).^[1] ^[2]

Publication Abstract from PubMed

The crystal structure of Escherichia coli dihydrodipicolinate synthase with pyruvate and substrate analogue succinic acid semi-aldehyde condensed with the active site lysine-161 was solved to a resolution of 2.3 A. Comparative analysis to a previously reported structure both resolves the configuration at the aldol addition centre, where the final addition product clearly displays the (S)-configuration, and the final conformation of the adduct within the active site. Direct comparison to two other crystal structures found in the Protein Data Bank, 1YXC and 3DU0, demonstrates significant similarity between the active site residues of these structures. Proteins 2012. (c) 2012 Wiley Periodicals, Inc.

The crystal structure of dihydrodipicolinate synthase from Escherichia coli with bound pyruvate and succinic acid semi-aldehyde: Unambiguous resolution of the stereochemistry of the condensation product.,Boughton BA, Dobson RC, Hutton CA Proteins. 2012 May 2. doi: 10.1002/prot.24106. PMID:22552955^[3]

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

References

↑ Devenish SR, Blunt JW, Gerrard JA. NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase. J Med Chem. 2010 Jun 24;53(12):4808-12. doi: 10.1021/jm100349s. PMID:20503968 doi:10.1021/jm100349s
↑ Blickling S, Renner C, Laber B, Pohlenz HD, Holak TA, Huber R. Reaction mechanism of Escherichia coli dihydrodipicolinate synthase investigated by X-ray crystallography and NMR spectroscopy. Biochemistry. 1997 Jan 7;36(1):24-33. PMID:8993314 doi:10.1021/bi962272d
↑ Boughton BA, Dobson RC, Hutton CA. The crystal structure of dihydrodipicolinate synthase from Escherichia coli with bound pyruvate and succinic acid semi-aldehyde: Unambiguous resolution of the stereochemistry of the condensation product. Proteins. 2012 May 2. doi: 10.1002/prot.24106. PMID:22552955 doi:10.1002/prot.24106

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Devenish SR, Blunt JW, Gerrard JA. NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase. J Med Chem. 2010 Jun 24;53(12):4808-12. doi: 10.1021/jm100349s. PMID:20503968 doi:10.1021/jm100349s

[2] Blickling S, Renner C, Laber B, Pohlenz HD, Holak TA, Huber R. Reaction mechanism of Escherichia coli dihydrodipicolinate synthase investigated by X-ray crystallography and NMR spectroscopy. Biochemistry. 1997 Jan 7;36(1):24-33. PMID:8993314 doi:10.1021/bi962272d

[3] Boughton BA, Dobson RC, Hutton CA. The crystal structure of dihydrodipicolinate synthase from Escherichia coli with bound pyruvate and succinic acid semi-aldehyde: Unambiguous resolution of the stereochemistry of the condensation product. Proteins. 2012 May 2. doi: 10.1002/prot.24106. PMID:22552955 doi:10.1002/prot.24106

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='4eou' size='340' side='right'caption='[[4eou]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4eou]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ubs 3ubs]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EOU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EOU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4eou]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ubs 3ubs]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EOU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EOU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
+</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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LYF:(2E,4S)-2-{[(5S)-5-AMINO-5-CARBOXYPENTYL]IMINO}-4-HYDROXYHEPTANEDIOIC+ACID'>LYF</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LYF:(2E,4S)-2-{[(5S)-5-AMINO-5-CARBOXYPENTYL]IMINO}-4-HYDROXYHEPTANEDIOIC+ACID'>LYF</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=4eou FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eou OCA], [https://pdbe.org/4eou PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4eou RCSB], [https://www.ebi.ac.uk/pdbsum/4eou PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4eou ProSAT]</span></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1yxc|1yxc]], [[3du0|3du0]], [[1dhp|1dhp]]</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4eou FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eou OCA], [http://pdbe.org/4eou PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4eou RCSB], [http://www.ebi.ac.uk/pdbsum/4eou PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4eou ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DAPA_ECOLI DAPA_ECOLI]] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).<ref>PMID:20503968</ref> <ref>PMID:8993314</ref>
+[[https://www.uniprot.org/uniprot/DAPA_ECOLI DAPA_ECOLI]] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).<ref>PMID:20503968</ref> <ref>PMID:8993314</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 28: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: 4-hydroxy-tetrahydrodipicolinate synthase]]
 [[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Boughton, B A]]
+[[Category: Boughton BA]]
-[[Category: Dobson, R C.J]]
+[[Category: Dobson RCJ]]
-[[Category: Hutton, C A]]
+[[Category: Hutton CA]]
-[[Category: Alpha/beta barrel]]
-[[Category: Amino-acid biosynthesis]]
-[[Category: Lyase]]
-[[Category: Schiff base]]
-[[Category: Tim barrel]]

4eou: Difference between revisions

Revision as of 07:21, 28 September 2022

Crystal structure of E. coli dihydrodipicolinate synthase with pyruvate and succinic semi-aldehyde bound in active site

Structural highlights

Function

Publication Abstract from PubMed

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References

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