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| | <StructureSection load='2c13' size='340' side='right'caption='[[2c13]], [[Resolution|resolution]] 2.15Å' scene=''> | | <StructureSection load='2c13' size='340' side='right'caption='[[2c13]], [[Resolution|resolution]] 2.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2c13]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C13 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C13 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2c13]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C13 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C13 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 2.15Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FHL:(E)-N~6~-[3-CARBOXY-1-(HYDROXYMETHYL)PROPYLIDENE]-L-LYSINE'>FHL</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FHL:(E)-N~6~-[3-CARBOXY-1-(HYDROXYMETHYL)PROPYLIDENE]-L-LYSINE'>FHL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1b4k|1b4k]], [[1gzg|1gzg]], [[1w54|1w54]], [[1w56|1w56]], [[1w5m|1w5m]], [[1w5n|1w5n]], [[1w5o|1w5o]], [[1w5p|1w5p]], [[1w5q|1w5q]], [[2c14|2c14]], [[2c15|2c15]], [[2c16|2c16]], [[2c18|2c18]], [[2c19|2c19]]</div></td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Porphobilinogen_synthase Porphobilinogen synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.24 4.2.1.24] </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=2c13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c13 OCA], [https://pdbe.org/2c13 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c13 RCSB], [https://www.ebi.ac.uk/pdbsum/2c13 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c13 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=2c13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c13 OCA], [https://pdbe.org/2c13 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c13 RCSB], [https://www.ebi.ac.uk/pdbsum/2c13 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c13 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/HEM2_PSEAE HEM2_PSEAE]] Catalyzes an early step in the biosynthesis of tetrapyrroles. Binds two molecules of 5-aminolevulinate per subunit, each at a distinct site, and catalyzes their condensation to form porphobilinogen (By similarity).
| + | [https://www.uniprot.org/uniprot/HEM2_PSEAE HEM2_PSEAE] Catalyzes an early step in the biosynthesis of tetrapyrroles. Binds two molecules of 5-aminolevulinate per subunit, each at a distinct site, and catalyzes their condensation to form porphobilinogen (By similarity). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Porphobilinogen synthase]] | + | [[Category: Pseudomonas aeruginosa]] |
| - | [[Category: Frankenberg-Dinkel, N]] | + | [[Category: Frankenberg-Dinkel N]] |
| - | [[Category: Frere, F]] | + | [[Category: Frere F]] |
| - | [[Category: Gacond, S]] | + | [[Category: Gacond S]] |
| - | [[Category: Heinz, D W]] | + | [[Category: Heinz DW]] |
| - | [[Category: Neier, R]] | + | [[Category: Neier R]] |
| - | [[Category: Nentwich, M]] | + | [[Category: Nentwich M]] |
| - | [[Category: Cocrystallization]]
| + | |
| - | [[Category: Enzyme mechanism]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Metalloenzyme]]
| + | |
| - | [[Category: Porphyrin biosynthesis]]
| + | |
| Structural highlights
2c13 is a 2 chain structure with sequence from Pseudomonas aeruginosa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.15Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
HEM2_PSEAE Catalyzes an early step in the biosynthesis of tetrapyrroles. Binds two molecules of 5-aminolevulinate per subunit, each at a distinct site, and catalyzes their condensation to form porphobilinogen (By similarity).
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
Porphobilinogen synthase catalyzes the first committed step of the tetrapyrrole biosynthesis pathway. In an aldol-like condensation, two molecules of 5-aminolevulinic acid (ALA) form the first pyrrole, porphobilinogen. Newly synthesized analogues of a reaction intermediate of porphobilinogen synthase have been employed in studying the active site and the catalytic mechanism of this early enzyme of tetrapyrrole biosynthesis. This study combines structural and kinetic evaluation of the inhibition potency of these inhibitors. In addition, one of the determined protein structures provides for the first time structural evidence of a magnesium ion in the active site. From these results, we can corroborate an earlier postulated enzymatic mechanism that starts with formation of a C-C bond, linking C3 of the A-side ALA to C4 of the P-side ALA through an aldole addition. The obtained data are discussed with respect to the current literature.
Probing the active site of Pseudomonas aeruginosa porphobilinogen synthase using newly developed inhibitors.,Frere F, Nentwich M, Gacond S, Heinz DW, Neier R, Frankenberg-Dinkel N Biochemistry. 2006 Jul 11;45(27):8243-53. PMID:16819823[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Frere F, Nentwich M, Gacond S, Heinz DW, Neier R, Frankenberg-Dinkel N. Probing the active site of Pseudomonas aeruginosa porphobilinogen synthase using newly developed inhibitors. Biochemistry. 2006 Jul 11;45(27):8243-53. PMID:16819823 doi:http://dx.doi.org/10.1021/bi052611f
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