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| | <StructureSection load='2sfp' size='340' side='right'caption='[[2sfp]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='2sfp' size='340' side='right'caption='[[2sfp]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2sfp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2SFP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2SFP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2sfp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2SFP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2SFP FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PPI:PROPANOIC+ACID'>PPI</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]] 1.9Å</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=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PPI:PROPANOIC+ACID'>PPI</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=2sfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2sfp OCA], [https://pdbe.org/2sfp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2sfp RCSB], [https://www.ebi.ac.uk/pdbsum/2sfp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2sfp 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=2sfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2sfp OCA], [https://pdbe.org/2sfp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2sfp RCSB], [https://www.ebi.ac.uk/pdbsum/2sfp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2sfp ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/ALR_GEOSE ALR_GEOSE]] Catalyzes the interconversion of L-alanine and D-alanine. Also weakly active on serine.<ref>PMID:10502689</ref> <ref>PMID:12203980</ref>
| + | [https://www.uniprot.org/uniprot/ALR_GEOSE ALR_GEOSE] Catalyzes the interconversion of L-alanine and D-alanine. Also weakly active on serine.<ref>PMID:10502689</ref> <ref>PMID:12203980</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: Alanine racemase]] | + | [[Category: Geobacillus stearothermophilus]] |
| - | [[Category: Atcc 12980]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Morollo, A A]] | + | [[Category: Morollo AA]] |
| - | [[Category: Petsko, G A]] | + | [[Category: Petsko GA]] |
| - | [[Category: Ringe, D]] | + | [[Category: Ringe D]] |
| - | [[Category: Alanine]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Pyridoxal phosphate]]
| + | |
| - | [[Category: Racemase]]
| + | |
| Structural highlights
Function
ALR_GEOSE Catalyzes the interconversion of L-alanine and D-alanine. Also weakly active on serine.[1] [2]
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 alanine racemase from Bacillus stearothermophilus with the inhibitor propionate bound in the active site was determined by X-ray crystallography to a resolution of 1.9 A. The enzyme is a homodimer in solution and crystallizes with a dimer in the asymmetric unit. Both active sites contain a pyridoxal 5'-phosphate (PLP) molecule in aldimine linkage to Lys39 as a protonated Schiff base, and the pH-independence of UV-visible absorption spectra suggests that the protonated PLP-Lys39 Schiff base is the reactive form of the enzyme. The carboxylate group of propionate bound in the active site makes numerous interactions with active-site residues, defining the substrate binding site of the enzyme. The propionate-bound structure therefore approximates features of the Michaelis complex formed between alanine racemase and its amino acid substrate. The structure also provides evidence for the existence of a carbamate formed on the side-chain amino group of Lys129, stabilized by interactions with one of the residues interacting with the carboxylate group of propionate, Arg136. We propose that this novel interaction influences both substrate binding and catalysis by precisely positioning Arg136 and modulating its charge.
Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase.,Morollo AA, Petsko GA, Ringe D Biochemistry. 1999 Mar 16;38(11):3293-301. PMID:10079072[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Watanabe A, Yoshimura T, Mikami B, Esaki N. Tyrosine 265 of alanine racemase serves as a base abstracting alpha-hydrogen from L-alanine: the counterpart residue to lysine 39 specific to D-alanine. J Biochem. 1999 Oct;126(4):781-6. PMID:10502689
- ↑ Patrick WM, Weisner J, Blackburn JM. Site-directed mutagenesis of Tyr354 in Geobacillus stearothermophilus alanine racemase identifies a role in controlling substrate specificity and a possible role in the evolution of antibiotic resistance. Chembiochem. 2002 Aug 2;3(8):789-92. PMID:12203980 doi:<789::AID-CBIC789>3.0.CO;2-D http://dx.doi.org/10.1002/1439-7633(20020802)3:8<789::AID-CBIC789>3.0.CO;2-D
- ↑ Morollo AA, Petsko GA, Ringe D. Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase. Biochemistry. 1999 Mar 16;38(11):3293-301. PMID:10079072 doi:10.1021/bi9822729
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