2vd9

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "2vd9" [edit=sysop:move=sysop])
Current revision (15:16, 13 December 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
[[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]]
+

Current revision

The crystal structure of alanine racemase from Bacillus anthracis (BA0252) with bound L-Ala-P

PDB ID 2vd9

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2vd9"
Personal tools