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| | <StructureSection load='1rcq' size='340' side='right'caption='[[1rcq]], [[Resolution|resolution]] 1.45Å' scene=''> | | <StructureSection load='1rcq' size='340' side='right'caption='[[1rcq]], [[Resolution|resolution]] 1.45Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1rcq]] is a 1 chain structure with sequence from [http://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=1RCQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1RCQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1rcq]] is a 1 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=1RCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RCQ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 1.45Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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;'>[[1sft|1sft]], [[1bdo|1bdo]], [[1epv|1epv]], [[1l6f|1l6f]], [[2sfp|2sfp]]</div></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=1rcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rcq OCA], [https://pdbe.org/1rcq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rcq RCSB], [https://www.ebi.ac.uk/pdbsum/1rcq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rcq ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dadx ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>
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| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1rcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rcq OCA], [http://pdbe.org/1rcq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rcq RCSB], [http://www.ebi.ac.uk/pdbsum/1rcq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rcq ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ALR2_PSEAE ALR2_PSEAE]] Isomerizes L-alanine to D-alanine which is then oxidized to pyruvate by DadA.<ref>PMID:10977898</ref> | + | [https://www.uniprot.org/uniprot/ALR2_PSEAE ALR2_PSEAE] Isomerizes L-alanine to D-alanine which is then oxidized to pyruvate by DadA.<ref>PMID:10977898</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rc/1rcq_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rc/1rcq_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Alanine racemase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Benedik, M]] | + | [[Category: Pseudomonas aeruginosa]] |
| - | [[Category: Dvorak, A]] | + | [[Category: Benedik M]] |
| - | [[Category: Im, H]] | + | [[Category: Dvorak A]] |
| - | [[Category: Krause, K L]] | + | [[Category: Im H]] |
| - | [[Category: Magueres, P Le]] | + | [[Category: Krause KL]] |
| - | [[Category: Strych, U]] | + | [[Category: Le Magueres P]] |
| - | [[Category: Alpha-beta barrel]]
| + | [[Category: Strych U]] |
| - | [[Category: Beta-structure for c-terminal domain]]
| + | |
| - | [[Category: Internal/external aldimine form]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| Structural highlights
Function
ALR2_PSEAE Isomerizes L-alanine to D-alanine which is then oxidized to pyruvate by DadA.[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
The structure of the catabolic alanine racemase, DadX, from the pathogenic bacterium Pseudomonas aeruginosa, reported here at 1.45 A resolution, is a dimer in which each monomer is comprised of two domains, an eight-stranded alpha/beta barrel containing the PLP cofactor and a second domain primarily composed of beta-strands. The geometry of each domain is very similar to that of Bacillus stearothermophilus alanine racemase, but the rotation between domains differs by about 15 degrees. This change does not alter the structure of the active site in which almost all residues superimpose well with a low rms difference of 0.86 A. Unexpectedly, the active site of DadX contains a guest substrate that is located where acetate and propionate have been observed in the Bacillus structures. It is modeled as d-lysine and oriented such that its terminal NZ atom makes a covalent bond with C4' of PLP. Since the internal aldimine bond between the protein lysine, Lys33, and C4' of PLP is also unambiguously observed, there appears to be an equilibrium between both internally and externally reacted forms. The PLP cofactor adopts two partially occupied conformational states that resemble previously reported internal and external aldimine complexes.
Crystal structure at 1.45 A resolution of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms.,LeMagueres P, Im H, Dvorak A, Strych U, Benedik M, Krause KL Biochemistry. 2003 Dec 23;42(50):14752-61. PMID:14674749[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Strych U, Huang HC, Krause KL, Benedik MJ. Characterization of the alanine racemases from Pseudomonas aeruginosa PAO1. Curr Microbiol. 2000 Oct;41(4):290-4. PMID:10977898
- ↑ LeMagueres P, Im H, Dvorak A, Strych U, Benedik M, Krause KL. Crystal structure at 1.45 A resolution of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms. Biochemistry. 2003 Dec 23;42(50):14752-61. PMID:14674749 doi:10.1021/bi030165v
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