2vd9: Difference between revisions

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<StructureSection load='2vd9' size='340' side='right'caption='[[2vd9]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='2vd9' size='340' side='right'caption='[[2vd9]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2vd9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_anthracis_(strain_ames) Bacillus anthracis (strain 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 [http://proteopedia.org/fgij/fg.htm?mol=2VD9 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2vd9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis_(strain_ames) Bacillus anthracis (strain 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>
</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></td></tr>
</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></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2vd8|2vd8]]</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2vd8|2vd8]]</div></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='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'>[http://proteopedia.org/fgij/fg.htm?mol=2vd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vd9 OCA], [http://pdbe.org/2vd9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vd9 RCSB], [http://www.ebi.ac.uk/pdbsum/2vd9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vd9 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=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>
</table>
== Evolutionary Conservation ==
== Evolutionary Conservation ==

Revision as of 14:34, 30 March 2022

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

Structural highlights

2vd9 is a 2 chain structure with sequence from Bacillus anthracis (strain ames). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , ,
NonStd Res:
Activity:Alanine racemase, with EC number 5.1.1.1
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

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.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Au K, Ren J, Walter TS, Harlos K, Nettleship JE, Owens RJ, Stuart DI, Esnouf RM. Structures of an alanine racemase from Bacillus anthracis (BA0252) in the presence and absence of (R)-1-aminoethylphosphonic acid (L-Ala-P). Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 May 1;64(Pt, 5):327-33. Epub 2008 Apr 5. PMID:18453697 doi:10.1107/S1744309108007252

2vd9, resolution 2.10Å

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