1w1a

From Proteopedia

(Difference between revisions)

Current revision

Structure of Bacillus subtilis PdaA in complex with NAG, a family 4 Carbohydrate esterase.

Structural highlights

1w1a is a 2 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.25Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PDAA_BACSU Catalyzes the deacetylation of N-acetylmuramic acid (MurNAc) residues in glycan strands of peptidoglycan, leading to the formation of muramic delta-lactam residues in spore cortex, after transpeptidation of deacetylated muramic acid residues. PdaA probably carries out both deacetylation and lactam ring formation and requires the product of CwlD activity on peptidoglycan as a substrate. Is required for germination. Cannot use chitin oligomer (hexa-N-acetylchitohexaose) as a substrate.^[1] ^[2] ^[3]

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

Family 4 carbohydrate esterases deacetylate polymeric carbohydrate substrates such as chitin, acetyl xylan and peptidoglycan. Although some of these enzymes have recently been enzymologically characterised, neither their structure nor their reaction mechanism has been defined. Sequence conservation in this family has pointed to a conserved core, termed the NodB homology domain. We describe the cloning, purification and 1.9 A crystal structure of PdaA, a peptidoglycan deacetylase from Bacillus subtilis. The enzyme assumes a fold related to a (beta/alpha)8 barrel, with a long groove on the surface of the protein that harbours all conserved residues. A complex with the substrate analogue N-acetyl-glucosamine was refined to 2.25 A resolution, revealing interactions of an aspartic acid and three histidines, all conserved in the NodB homology domain, with the ligand. The PdaA structure provides a template for interpreting the wealth of sequence data on family 4 carbohydrate esterases in a structural context and represents a first step towards understanding the reaction mechanism of this family of enzymes.

Structures of Bacillus subtilis PdaA, a family 4 carbohydrate esterase, and a complex with N-acetyl-glucosamine.,Blair DE, van Aalten DM FEBS Lett. 2004 Jul 16;570(1-3):13-9. PMID:15251431^[4]

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

References

↑ Fukushima T, Yamamoto H, Atrih A, Foster SJ, Sekiguchi J. A polysaccharide deacetylase gene (pdaA) is required for germination and for production of muramic delta-lactam residues in the spore cortex of Bacillus subtilis. J Bacteriol. 2002 Nov;184(21):6007-15. PMID:12374835
↑ Gilmore ME, Bandyopadhyay D, Dean AM, Linnstaedt SD, Popham DL. Production of muramic delta-lactam in Bacillus subtilis spore peptidoglycan. J Bacteriol. 2004 Jan;186(1):80-9. PMID:14679227
↑ Fukushima T, Kitajima T, Sekiguchi J. A polysaccharide deacetylase homologue, PdaA, in Bacillus subtilis acts as an N-acetylmuramic acid deacetylase in vitro. J Bacteriol. 2005 Feb;187(4):1287-92. PMID:15687192 doi:http://dx.doi.org/10.1128/JB.187.4.1287-1292.2005
↑ Blair DE, van Aalten DM. Structures of Bacillus subtilis PdaA, a family 4 carbohydrate esterase, and a complex with N-acetyl-glucosamine. FEBS Lett. 2004 Jul 16;570(1-3):13-9. PMID:15251431 doi:http://dx.doi.org/10.1016/j.febslet.2004.06.013

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1w1a"

Categories: Bacillus subtilis | Large Structures | Blair DE | Van Aalten DMF

@@ Line 3: / Line 3: @@
 <StructureSection load='1w1a' size='340' side='right'caption='[[1w1a]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1w1a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W1A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W1A FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1w1a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W1A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W1A FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</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]] 2.25&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ny1|1ny1]], [[1w17|1w17]], [[1w1b|1w1b]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></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=1w1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w1a OCA], [https://pdbe.org/1w1a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w1a RCSB], [https://www.ebi.ac.uk/pdbsum/1w1a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w1a ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PDAA_BACSU PDAA_BACSU] Catalyzes the deacetylation of N-acetylmuramic acid (MurNAc) residues in glycan strands of peptidoglycan, leading to the formation of muramic delta-lactam residues in spore cortex, after transpeptidation of deacetylated muramic acid residues. PdaA probably carries out both deacetylation and lactam ring formation and requires the product of CwlD activity on peptidoglycan as a substrate. Is required for germination. Cannot use chitin oligomer (hexa-N-acetylchitohexaose) as a substrate.<ref>PMID:12374835</ref> <ref>PMID:14679227</ref> <ref>PMID:15687192</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Vibrio subtilis ehrenberg 1835]]
+[[Category: Bacillus subtilis]]
 [[Category: Large Structures]]
-[[Category: Aalten, D M.F van]]
+[[Category: Blair DE]]
-[[Category: Blair, D E]]
+[[Category: Van Aalten DMF]]
-[[Category: Deacetylase]]
-[[Category: Family 4 carbohydrate esterase]]
-[[Category: Hydrolase]]
-[[Category: Nodb homology domain]]
-[[Category: Peptidoglycan]]
-[[Category: Sporulation]]

1w1a

From Proteopedia

Current revision

Structure of Bacillus subtilis PdaA in complex with NAG, a family 4 Carbohydrate esterase.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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