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| | ==Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate== | | ==Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate== |
| - | <StructureSection load='3kw3' size='340' side='right' caption='[[3kw3]], [[Resolution|resolution]] 2.04Å' scene=''> | + | <StructureSection load='3kw3' size='340' side='right'caption='[[3kw3]], [[Resolution|resolution]] 2.04Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3kw3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_49882 Atcc 49882]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KW3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KW3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3kw3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bartonella_henselae Bartonella henselae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KW3 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</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]] 2.04Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">alr, BH12810 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=38323 ATCC 49882])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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='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'>[https://proteopedia.org/fgij/fg.htm?mol=3kw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kw3 OCA], [https://pdbe.org/3kw3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kw3 RCSB], [https://www.ebi.ac.uk/pdbsum/3kw3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kw3 ProSAT]</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=3kw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kw3 OCA], [http://pdbe.org/3kw3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kw3 RCSB], [http://www.ebi.ac.uk/pdbsum/3kw3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kw3 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q6G2F2_BARHE Q6G2F2_BARHE]] Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids (By similarity).[HAMAP-Rule:MF_01201] | + | [https://www.uniprot.org/uniprot/A0A0H3LZE4_BARHE A0A0H3LZE4_BARHE] Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids.[HAMAP-Rule:MF_01201] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kw/3kw3_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kw/3kw3_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | ==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: Bartonella henselae]] |
| - | [[Category: Atcc 49882]] | + | [[Category: Large Structures]] |
| - | [[Category: Structural genomic]]
| + | |
| - | [[Category: Cat-scratch disease]]
| + | |
| - | [[Category: Iodide soak]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Llp]]
| + | |
| - | [[Category: Niaid]]
| + | |
| - | [[Category: Ssgcid]]
| + | |
| Structural highlights
Function
A0A0H3LZE4_BARHE Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids.[HAMAP-Rule:MF_01201]
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 Seattle Structural Genomics Center for Infectious Disease (SSGCID) focuses on the structure elucidation of potential drug targets from class A, B, and C infectious disease organisms. Many SSGCID targets are selected because they have homologs in other organisms that are validated drug targets with known structures. Thus, many SSGCID targets are expected to be solved by molecular replacement (MR), and reflective of this, all proteins are expressed in native form. However, many community request targets do not have homologs with known structures and not all internally selected targets readily solve by MR, necessitating experimental phase determination. We have adopted the use of iodide ion soaks and single wavelength anomalous dispersion (SAD) experiments as our primary method for de novo phasing. This method uses existing native crystals and in house data collection, resulting in rapid, low cost structure determination. Iodide ions are non-toxic and soluble at molar concentrations, facilitating binding at numerous hydrophobic or positively charged sites. We have used this technique across a wide range of crystallization conditions with successful structure determination in 16 of 17 cases within the first year of use (94% success rate). Here we present a general overview of this method as well as several examples including SAD phasing of proteins with novel folds and the combined use of SAD and MR for targets with weak MR solutions. These cases highlight the straightforward and powerful method of iodide ion SAD phasing in a high-throughput structural genomics environment.
SAD phasing using iodide ions in a high-throughput structural genomics environment.,Abendroth J, Gardberg AS, Robinson JI, Christensen JS, Staker BL, Myler PJ, Stewart LJ, Edwards TE J Struct Funct Genomics. 2011 Jul;12(2):83-95. Epub 2011 Feb 27. PMID:21359836[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Abendroth J, Gardberg AS, Robinson JI, Christensen JS, Staker BL, Myler PJ, Stewart LJ, Edwards TE. SAD phasing using iodide ions in a high-throughput structural genomics environment. J Struct Funct Genomics. 2011 Jul;12(2):83-95. Epub 2011 Feb 27. PMID:21359836 doi:10.1007/s10969-011-9101-7
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