3ga9: Difference between revisions

Latest revision as of 01:50, 21 November 2024

Crystal structure of Bacillus anthracis transpeptidase enzyme CapD, crystal form II

Structural highlights

3ga9 is a 2 chain structure with sequence from Bacillus anthracis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:	GLU, MSE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAPD_BACAN Degradation of the high-molecular weight capsule (H-capsule) to the lower-molecular weight capsule (L-capsule), which is released from the bacterial cell surface. The production of L-capsule is essential to mediate escape from host defenses. Does not have gamma-glutamyltranspeptidase (GGT) activity.^[1] ^[2]

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 elaborates a poly-gamma-d-glutamic acid capsule that protects bacilli from phagocytic killing during infection. The enzyme CapD generates amide bonds with peptidoglycan cross-bridges to anchor capsular material within the cell wall envelope of B. anthracis. The capsular biosynthetic pathway is essential for virulence during anthrax infections and can be targeted for anti-infective inhibition with small molecules. Here, we present the crystal structures of the gamma-glutamyltranspeptidase CapD with and without alpha-l-Glu-l-Glu dipeptide, a non-hydrolyzable analog of poly-gamma-d-glutamic acid, in the active site. Purified CapD displays transpeptidation activity in vitro, and its structure reveals an active site broadly accessible for poly-gamma-glutamate binding and processing. Using structural and biochemical information, we derive a mechanistic model for CapD catalysis whereby Pro(427), Gly(428), and Gly(429) activate the catalytic residue of the enzyme, Thr(352), and stabilize an oxyanion hole via main chain amide hydrogen bonds.

Crystal structure of Bacillus anthracis transpeptidase enzyme CapD.,Wu R, Richter S, Zhang RG, Anderson VJ, Missiakas D, Joachimiak A J Biol Chem. 2009 Sep 4;284(36):24406-14. Epub 2009 Jun 16. PMID:19535342^[3]

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

References

↑ Uchida I, Makino S, Sasakawa C, Yoshikawa M, Sugimoto C, Terakado N. Identification of a novel gene, dep, associated with depolymerization of the capsular polymer in Bacillus anthracis. Mol Microbiol. 1993 Aug;9(3):487-96. PMID:8105361
↑ Makino S, Watarai M, Cheun HI, Shirahata T, Uchida I. Effect of the lower molecular capsule released from the cell surface of Bacillus anthracis on the pathogenesis of anthrax. J Infect Dis. 2002 Jul 15;186(2):227-33. Epub 2002 Jun 27. PMID:12134259 doi:https://dx.doi.org/JID020035
↑ Wu R, Richter S, Zhang RG, Anderson VJ, Missiakas D, Joachimiak A. Crystal structure of Bacillus anthracis transpeptidase enzyme CapD. J Biol Chem. 2009 Sep 4;284(36):24406-14. Epub 2009 Jun 16. PMID:19535342 doi:10.1074/jbc.M109.019034

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OCA

[1] Uchida I, Makino S, Sasakawa C, Yoshikawa M, Sugimoto C, Terakado N. Identification of a novel gene, dep, associated with depolymerization of the capsular polymer in Bacillus anthracis. Mol Microbiol. 1993 Aug;9(3):487-96. PMID:8105361

[2] Makino S, Watarai M, Cheun HI, Shirahata T, Uchida I. Effect of the lower molecular capsule released from the cell surface of Bacillus anthracis on the pathogenesis of anthrax. J Infect Dis. 2002 Jul 15;186(2):227-33. Epub 2002 Jun 27. PMID:12134259 doi:https://dx.doi.org/JID020035

[3] Wu R, Richter S, Zhang RG, Anderson VJ, Missiakas D, Joachimiak A. Crystal structure of Bacillus anthracis transpeptidase enzyme CapD. J Biol Chem. 2009 Sep 4;284(36):24406-14. Epub 2009 Jun 16. PMID:19535342 doi:10.1074/jbc.M109.019034

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Crystal structure of Bacillus anthracis transpeptidase enzyme CapD, crystal form II==
-<StructureSection load='3ga9' size='340' side='right' caption='[[3ga9]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='3ga9' size='340' side='right'caption='[[3ga9]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ga9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cereus_var._anthracis"_(cohn_1872)_smith_et_al._1946 "bacillus cereus var. anthracis" (cohn 1872) smith et al. 1946]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GA9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GA9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ga9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GA9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GA9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</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]] 2.3&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3g9k|3g9k]]</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=3ga9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ga9 OCA], [https://pdbe.org/3ga9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ga9 RCSB], [https://www.ebi.ac.uk/pdbsum/3ga9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ga9 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BAK_B0097, BXB0063, capD, dep, GBAA_pXO2_0063, pXO2-55 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 "Bacillus cereus var. anthracis" (Cohn 1872) Smith et al. 1946]), capD, dep, pXO2-55, BXB0063, GBAA_pXO2_0063 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 "Bacillus cereus var. anthracis" (Cohn 1872) Smith et al. 1946])</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=3ga9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ga9 OCA], [http://pdbe.org/3ga9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ga9 RCSB], [http://www.ebi.ac.uk/pdbsum/3ga9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ga9 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CAPD_BACAN CAPD_BACAN]] Degradation of the high-molecular weight capsule (H-capsule) to the lower-molecular weight capsule (L-capsule), which is released from the bacterial cell surface. The production of L-capsule is essential to mediate escape from host defenses. Does not have gamma-glutamyltranspeptidase (GGT) activity.<ref>PMID:8105361</ref> <ref>PMID:12134259</ref>
+[https://www.uniprot.org/uniprot/CAPD_BACAN CAPD_BACAN] Degradation of the high-molecular weight capsule (H-capsule) to the lower-molecular weight capsule (L-capsule), which is released from the bacterial cell surface. The production of L-capsule is essential to mediate escape from host defenses. Does not have gamma-glutamyltranspeptidase (GGT) activity.<ref>PMID:8105361</ref> <ref>PMID:12134259</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 17: / Line 15: @@
    <jmolCheckbox>
      <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ga/3ga9_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 35: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Anderson, V J]]
-[[Category: Joachimiak, A]]
-[[Category: Missiakas, D]]
-[[Category: Richter, S]]
-[[Category: Wu, R]]
-[[Category: Zhang, R]]
 [[Category: Bacillus anthracis]]
-[[Category: Capd protein]]
+[[Category: Large Structures]]
-[[Category: Capsule biogenesis/degradation]]
+[[Category: Anderson VJ]]
-[[Category: Glrce]]
+[[Category: Joachimiak A]]
-[[Category: Hydrolase]]
+[[Category: Missiakas D]]
-[[Category: The great lakes regional center of excellence]]
+[[Category: Richter S]]
-[[Category: Virulence]]
+[[Category: Wu R]]
+[[Category: Zhang R]]

3ga9: Difference between revisions

Latest revision as of 01:50, 21 November 2024

Crystal structure of Bacillus anthracis transpeptidase enzyme CapD, crystal form II

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

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