2vd9: Difference between revisions

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-[[Image:2vd9.png|left|200px]]
-<!--
+==The crystal structure of alanine racemase from Bacillus anthracis (BA0252) with bound L-Ala-P==
-The line below this paragraph, containing "STRUCTURE_2vd9", creates the "Structure Box" on the page.
+<StructureSection load='2vd9' size='340' side='right'caption='[[2vd9]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2vd9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis_str._Ames Bacillus anthracis str. Ames]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VD9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VD9 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</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=EPC:(1S)-1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLENE)AMINO]ETHYLPHOSPHONIC+ACID'>EPC</scene>, <scene name='pdbligand=IN5:{1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONIC+ACID'>IN5</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
-{{STRUCTURE_2vd9|  PDB=2vd9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vd9 OCA], [https://pdbe.org/2vd9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vd9 RCSB], [https://www.ebi.ac.uk/pdbsum/2vd9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vd9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A6L7HC45_BACAN A0A6L7HC45_BACAN] Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids.[HAMAP-Rule:MF_01201]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vd/2vd9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vd9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Bacillus anthracis, the causative agent of anthrax, has been targeted by the Oxford Protein Production Facility to validate high-throughput protocols within the Structural Proteomics in Europe project. As part of this work, the structures of an alanine racemase (BA0252) in the presence and absence of the inhibitor (R)-1-aminoethylphosphonic acid (L-Ala-P) have determined by X-ray crystallography to resolutions of 2.1 and 1.47 A, respectively. Difficulties in crystallizing this protein were overcome by the use of reductive methylation. Alanine racemase has attracted much interest as a possible target for anti-anthrax drugs: not only is D-alanine a vital component of the bacterial cell wall, but recent studies also indicate that alanine racemase, which is accessible in the exosporium, plays a key role in inhibition of germination in B. anthracis. These structures confirm the binding mode of L-Ala-P but suggest an unexpected mechanism of inhibition of alanine racemase by this compound and could provide a basis for the design of improved alanine racemase inhibitors with potential as anti-anthrax therapies.
-===The crystal structure of alanine racemase from Bacillus anthracis (BA0252) with bound L-Ala-P===
+Structures of an alanine racemase from Bacillus anthracis (BA0252) in the presence and absence of (R)-1-aminoethylphosphonic acid (L-Ala-P).,Au K, Ren J, Walter TS, Harlos K, Nettleship JE, Owens RJ, Stuart DI, Esnouf RM Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 May 1;64(Pt, 5):327-33. Epub 2008 Apr 5. PMID:18453697<ref>PMID:18453697</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2vd9" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18453697}}, adds the Publication Abstract to the page
+*[[Alanine racemase 3D structures|Alanine racemase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18453697 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18453697}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Bacillus anthracis str. Ames]]
-[[2vd9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VD9 OCA].
+[[Category: Large Structures]]
+[[Category: Au K]]
-==Reference==
+[[Category: Esnouf RM]]
-<ref group="xtra">PMID:018453697</ref><references group="xtra"/>
+[[Category: Harlos K]]
-[[Category: Alanine racemase]]
+[[Category: Nettleship JE]]
-[[Category: Bacillus anthracis]]
+[[Category: Owens RJ]]
-[[Category: Au, K.]]
+[[Category: Ren J]]
-[[Category: Esnouf, R M.]]
+[[Category: Stuart DI]]
-[[Category: Harlos, K.]]
+[[Category: Walter TS]]
-[[Category: Nettleship, J E.]]
-[[Category: Oppf, Oxford Protein Production Facility.]]
-[[Category: Owens, R J.]]
-[[Category: Ren, J.]]
-[[Category: Spine, Structural Proteomics in Europe.]]
-[[Category: Stuart, D I.]]
-[[Category: Walter, T S.]]
-[[Category: Alanine racemase]]
-[[Category: D-alanine]]
-[[Category: Isomerase]]
-[[Category: L-alanine]]
-[[Category: Oppf]]
-[[Category: Oxford protein production facility]]
-[[Category: Peptidoglycan synthesis]]
-[[Category: Plp]]
-[[Category: Pyridoxal 5'-phosphate]]
-[[Category: Pyridoxal phosphate]]
-[[Category: Spore germination]]
-[[Category: Structural genomic]]