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| | <StructureSection load='3isz' size='340' side='right'caption='[[3isz]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='3isz' size='340' side='right'caption='[[3isz]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3isz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Haein Haein]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ISZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ISZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3isz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae_Rd_KW20 Haemophilus influenzae Rd KW20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ISZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ISZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ic1|3ic1]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapE, HI0102 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 HAEIN])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Succinyl-diaminopimelate_desuccinylase Succinyl-diaminopimelate desuccinylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.18 3.5.1.18] </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=3isz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3isz OCA], [https://pdbe.org/3isz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3isz RCSB], [https://www.ebi.ac.uk/pdbsum/3isz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3isz ProSAT]</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=3isz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3isz OCA], [https://pdbe.org/3isz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3isz RCSB], [https://www.ebi.ac.uk/pdbsum/3isz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3isz ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/DAPE_HAEIN DAPE_HAEIN]] Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls. It can only hydrolyze L,L-N-succinyl-diaminopimelic acid (L,L-SDAP) and is inactive toward D,L-, L,D-, and D,D-SDAP.<ref>PMID:12962500</ref> <ref>PMID:16421726</ref> <ref>PMID:18712420</ref>
| + | [https://www.uniprot.org/uniprot/DAPE_HAEIN DAPE_HAEIN] Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls. It can only hydrolyze L,L-N-succinyl-diaminopimelic acid (L,L-SDAP) and is inactive toward D,L-, L,D-, and D,D-SDAP.<ref>PMID:12962500</ref> <ref>PMID:16421726</ref> <ref>PMID:18712420</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Haein]] | + | [[Category: Haemophilus influenzae Rd KW20]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Succinyl-diaminopimelate desuccinylase]]
| + | [[Category: Gillner DM]] |
| - | [[Category: Gillner, D M]] | + | [[Category: Holz RC]] |
| - | [[Category: Holz, R C]] | + | [[Category: Joachimiak A]] |
| - | [[Category: Joachimiak, A]] | + | [[Category: Nocek BP]] |
| - | [[Category: Structural genomic]]
| + | |
| - | [[Category: Nocek, B P]] | + | |
| - | [[Category: Amino-acid biosynthesis]]
| + | |
| - | [[Category: Cobalt]]
| + | |
| - | [[Category: Dape]]
| + | |
| - | [[Category: Diaminopimelate biosynthesis]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Lysine biosynthesis]]
| + | |
| - | [[Category: Mcsg]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Metallopeptidase]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| - | [[Category: Zn-binding]]
| + | |
| Structural highlights
Function
DAPE_HAEIN Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls. It can only hydrolyze L,L-N-succinyl-diaminopimelic acid (L,L-SDAP) and is inactive toward D,L-, L,D-, and D,D-SDAP.[1] [2] [3]
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
Biosynthesis of lysine and meso-diaminopimelic acid in bacteria provides essential components for protein synthesis and construction of the bacterial peptidoglycan cell wall. The dapE operon enzymes synthesize both meso-diaminopimelic acid and lysine and, therefore, represent potential targets for novel antibacterials. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase functions in a late step of the pathway and converts N-succinyl-L,L-diaminopimelic acid to L,L-diaminopimelic acid and succinate. Deletion of the dapE gene is lethal to Helicobacter pylori and Mycobacterium smegmatis, indicating that DapE's are essential for cell growth and proliferation. Since there are no similar pathways in humans, inhibitors that target DapE may have selective toxicity against only bacteria. A major limitation in developing antimicrobial agents that target DapE has been the lack of structural information. Herein, we report the high-resolution X-ray crystal structures of the DapE from Haemophilus influenzae with one and two zinc ions bound in the active site, respectively. These two forms show different activity. Based on these newly determined structures, we propose a revised catalytic mechanism of peptide bond cleavage by DapE enzymes. These structures provide important insight into catalytic mechanism of DapE enzymes as well as a structural foundation that is critical for the rational design of DapE inhibitors.
Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase.,Nocek BP, Gillner DM, Fan Y, Holz RC, Joachimiak A J Mol Biol. 2010 Apr 2;397(3):617-26. Epub 2010 Feb 4. PMID:20138056[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Bienvenue DL, Gilner DM, Davis RS, Bennett B, Holz RC. Substrate specificity, metal binding properties, and spectroscopic characterization of the DapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Haemophilus influenzae. Biochemistry. 2003 Sep 16;42(36):10756-63. PMID:12962500 doi:http://dx.doi.org/10.1021/bi034845+
- ↑ Davis R, Bienvenue D, Swierczek SI, Gilner DM, Rajagopal L, Bennett B, Holz RC. Kinetic and spectroscopic characterization of the E134A- and E134D-altered dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Haemophilus influenzae. J Biol Inorg Chem. 2006 Mar;11(2):206-16. Epub 2006 Jan 19. PMID:16421726 doi:10.1007/s00775-005-0071-8
- ↑ Gillner DM, Bienvenue DL, Nocek BP, Joachimiak A, Zachary V, Bennett B, Holz RC. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Haemophilus influenzae contains two active-site histidine residues. J Biol Inorg Chem. 2009 Jan;14(1):1-10. doi: 10.1007/s00775-008-0418-z. Epub 2008, Aug 19. PMID:18712420 doi:10.1007/s00775-008-0418-z
- ↑ Nocek BP, Gillner DM, Fan Y, Holz RC, Joachimiak A. Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase. J Mol Biol. 2010 Apr 2;397(3):617-26. Epub 2010 Feb 4. PMID:20138056 doi:10.1016/j.jmb.2010.01.062
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