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| | ==CRYSTAL STRUCTURE OF 4-AMINO-4-DEOXYCHORISMATE LYASE FROM PSEUDOMONAS AERUGINOSA== | | ==CRYSTAL STRUCTURE OF 4-AMINO-4-DEOXYCHORISMATE LYASE FROM PSEUDOMONAS AERUGINOSA== |
| - | <StructureSection load='2y4r' size='340' side='right' caption='[[2y4r]], [[Resolution|resolution]] 1.75Å' scene=''> | + | <StructureSection load='2y4r' size='340' side='right'caption='[[2y4r]], [[Resolution|resolution]] 1.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2y4r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2y1u 2y1u] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2xpf 2xpf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Y4R FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2y4r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseae Pseae]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2y1u 2y1u] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2xpf 2xpf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y4R FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminodeoxychorismate_lyase Aminodeoxychorismate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.38 4.1.3.38] </span></td></tr> | + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aminodeoxychorismate_lyase Aminodeoxychorismate lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.38 4.1.3.38] </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=2y4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y4r OCA], [http://pdbe.org/2y4r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2y4r RCSB], [http://www.ebi.ac.uk/pdbsum/2y4r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2y4r 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=2y4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y4r OCA], [https://pdbe.org/2y4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y4r RCSB], [https://www.ebi.ac.uk/pdbsum/2y4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y4r ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Aminodeoxychorismate lyase]] | | [[Category: Aminodeoxychorismate lyase]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Pseae]] | | [[Category: Pseae]] |
| | [[Category: Agacan, M]] | | [[Category: Agacan, M]] |
| Structural highlights
2y4r is a 2 chain structure with sequence from Pseae. This structure supersedes the now removed PDB entries 2y1u and 2xpf. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , , , , |
| Activity: | Aminodeoxychorismate lyase, with EC number 4.1.3.38 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Publication Abstract from PubMed
4-Amino-4-deoxychorismate lyase (PabC) catalyzes the formation of 4-aminobenzoate, and release of pyruvate, during folate biosynthesis. This is an essential activity for the growth of Gram-negative bacteria, including important pathogens such as Pseudomonas aeruginosa. A high-resolution (1.75 A) crystal structure of PabC from P. aeruginosa has been determined, and sequence-structure comparisons with orthologous structures are reported. Residues around the pyridoxal 5'-phosphate cofactor are highly conserved adding support to aspects of a mechanism generic for enzymes carrying that cofactor. However, we suggest that PabC can be classified into two groups depending upon whether an active site and structurally conserved tyrosine is provided from the polypeptide that mainly forms an active site or from the partner subunit in the dimeric assembly. We considered that the conserved tyrosine might indicate a direct role in catalysis: that of providing a proton to reduce the olefin moiety of substrate as pyruvate is released. A threonine had previously been suggested to fulfill such a role prior to our observation of the structurally conserved tyrosine. We have been unable to elucidate an experimentally determined structure of PabC in complex with ligands to inform on mechanism and substrate specificity. Therefore we constructed a computational model of the catalytic intermediate docked into the enzyme active site. The model suggests that the conserved tyrosine helps to create a hydrophobic wall on one side of the active site that provides important interactions to bind the catalytic intermediate. However, this residue does not appear to participate in interactions with the C atom that undergoes an sp(2) to sp(3) conversion as pyruvate is produced. The model and our comparisons rather support the hypothesis that an active site threonine hydroxyl contributes a proton used in the reduction of the substrate methylene to pyruvate methyl in the final stage of the mechanism.
Pseudomonas aeruginosa 4-Amino-4-Deoxychorismate Lyase: Spatial Conservation of an Active Site Tyrosine and Classification of Two Types of Enzyme.,O'Rourke PE, Eadsforth TC, Fyfe PK, Shepherd SM, Hunter WN PLoS One. 2011;6(9):e24158. Epub 2011 Sep 15. PMID:21935381[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ O'Rourke PE, Eadsforth TC, Fyfe PK, Shepherd SM, Hunter WN. Pseudomonas aeruginosa 4-Amino-4-Deoxychorismate Lyase: Spatial Conservation of an Active Site Tyrosine and Classification of Two Types of Enzyme. PLoS One. 2011;6(9):e24158. Epub 2011 Sep 15. PMID:21935381 doi:10.1371/journal.pone.0024158
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