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| | ==The crystal structure of alanine racemase from streptococcus pneumoniae== | | ==The crystal structure of alanine racemase from streptococcus pneumoniae== |
| - | <StructureSection load='3s46' size='340' side='right' caption='[[3s46]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='3s46' size='340' side='right'caption='[[3s46]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3s46]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3mub 3mub]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S46 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3s46]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3mub 3mub]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S46 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S46 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</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='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>, <scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">alaR, alr, SP_1698 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1313 Streptococcus pneumoniae])</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=3s46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s46 OCA], [https://pdbe.org/3s46 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s46 RCSB], [https://www.ebi.ac.uk/pdbsum/3s46 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s46 ProSAT]</span></td></tr> |
| - | <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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3s46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s46 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s46 RCSB], [http://www.ebi.ac.uk/pdbsum/3s46 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/ALR_STRPN ALR_STRPN] Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3s46" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Alanine racemase|Alanine racemase]] | + | *[[Alanine racemase 3D structures|Alanine racemase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Alanine racemase]] | + | [[Category: Large Structures]] |
| | [[Category: Streptococcus pneumoniae]] | | [[Category: Streptococcus pneumoniae]] |
| - | [[Category: Davlieva, M]] | + | [[Category: Davlieva M]] |
| - | [[Category: Im, H]] | + | [[Category: Im H]] |
| - | [[Category: Krause, K L]] | + | [[Category: Krause KL]] |
| - | [[Category: Sharpe, M L]] | + | [[Category: Sharpe ML]] |
| - | [[Category: Strych, U]] | + | [[Category: Strych U]] |
| - | [[Category: Alpha/beta barrel]]
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| - | [[Category: Carbamylated lysine]]
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| - | [[Category: Extended beta-strand domain]]
| + | |
| - | [[Category: Isomerase]]
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| - | [[Category: Pyridoxal phosphate cofactor]]
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| Structural highlights
Function
ALR_STRPN Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids (By similarity).
Publication Abstract from PubMed
ABSTRACT: BACKGROUND: Streptococcus pneumoniae is a globally important pathogen. The Gram-positive diplococcus is a leading cause of pneumonia, otitis media, bacteremia, and meningitis, and antibiotic resistant strains have become increasingly common over recent years. Alanine racemase is a ubiquitous enzyme among bacteria and provides the essential cell wall precursor, D-alanine. Since it is absent in humans, this enzyme is an attractive target for the development of drugs against S. pneumoniae and other bacterial pathogens. RESULTS: Here we report the crystal structure of alanine racemase from S. pneumoniae (AlrSP). Crystals diffracted to a resolution of 2.0 A and belong to the space group P3121 with the unit cell parameters a=b=119.97 A, c=118.10 A, alpha=beta=90degrees and gamma=120degrees. Structural comparisons show that AlrSP shares both an overall fold and key active site residues with other bacterial alanine racemases. The active site cavity is similar to other Gram positive alanine racemases, featuring a restricted but conserved entryway. CONCLUSIONS: We have solved the structure of AlrSP, an essential step towards the development of an accurate pharmacophore model of the enzyme, and an important contribution towards our on-going alanine racemase structure-based drug design project. We have identified three regions on the enzyme that could be targeted for inhibitor design, the active site, the dimer interface, and the active site entryway.
The crystal structure of alanine racemase from Streptococcus pneumoniae, a target for structure-based drug design.,Im H, Sharpe ML, Strych U, Davlieva M, Krause KL BMC Microbiol. 2011 May 25;11(1):116. PMID:21612658[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Im H, Sharpe ML, Strych U, Davlieva M, Krause KL. The crystal structure of alanine racemase from Streptococcus pneumoniae, a target for structure-based drug design. BMC Microbiol. 2011 May 25;11(1):116. PMID:21612658 doi:10.1186/1471-2180-11-116
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