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4j2o

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Revision as of 21:27, 16 November 2022

Crystal structure of NADP-bound WbjB from A. baumannii community strain D1279779

Structural highlights

4j2o is a 6 chain structure with sequence from Acinetobacter baumannii D1279779. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PYRRH_PYRAP Antibacterial peptide. Affects Gram-negative bacteria E.coli 1106, P.aeruginosa, E.coli D22 and E.cloacae and Gram-positive bacteria M.luteus and B.subtilis.

Publication Abstract from PubMed

With new strains of Acinetobacter baumannii undergoing genomic analysis, it has been possible to define regions of genomic plasticity (RGPs), encoding specific adaptive elements. For a selected RGP from a community-derived isolate of A. baumannii, we outline sequences compatible with biosynthetic machinery of surface polysaccharides, specifically enzymes utilized in the dehydration and conversion of UDP-N-acetyl-D-glucosamine (UDP-D-GlcNAc). We have determined the crystal structure of one of these, the epimerase Ab-WbjB. This dehydratase belongs to the 'extended' short-chain dehydrogenase/reductase (SDR) family, related in fold to previously characterised enzymes CapE and FlaA1. Our 2.65A resolution structure of Ab-WbjB shows a hexamer, organised into a trimer of chain pairs, with coenzyme NADP+ occupying each chain. Specific active-site interactions between each coenzyme and a lysine quaternary group of a neighbouring chain interconnect adjacent dimers, so stabilising the hexameric form. We show UDP-GlcNAc to be a specific substrate for Ab-WbjB, with binding evident by ITC (Ka = 0.23 mumol-1). The sequence of Ab-WbjB shows variation from the consensus active-site motifs of many SDR enzymes, demonstrating a likely catalytic role for a specific threonine sidechain (as an alternative to tyrosine) in the canonical active site chemistry of these epimerases.

Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii.,Shah BS, Ashwood HE, Harrop SJ, Farrugia DN, Paulsen IT, Mabbutt BC PLoS One. 2018 Jan 19;13(1):e0191610. doi: 10.1371/journal.pone.0191610., eCollection 2018. PMID:29352301^[1]

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

References

↑ Shah BS, Ashwood HE, Harrop SJ, Farrugia DN, Paulsen IT, Mabbutt BC. Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii. PLoS One. 2018 Jan 19;13(1):e0191610. doi: 10.1371/journal.pone.0191610., eCollection 2018. PMID:29352301 doi:http://dx.doi.org/10.1371/journal.pone.0191610

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4j2o"

@@ Line 3: / Line 3: @@
 <StructureSection load='4j2o' size='340' side='right'caption='[[4j2o]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4j2o]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_baumannii_d1279779 Acinetobacter baumannii d1279779]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J2O OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4J2O FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4j2o]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii_D1279779 Acinetobacter baumannii D1279779]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J2O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J2O FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4j2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j2o OCA], [https://pdbe.org/4j2o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j2o RCSB], [https://www.ebi.ac.uk/pdbsum/4j2o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j2o ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ACIN5098_0096 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=945556 Acinetobacter baumannii D1279779])</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=4j2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j2o OCA], [http://pdbe.org/4j2o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4j2o RCSB], [http://www.ebi.ac.uk/pdbsum/4j2o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4j2o ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PYRRH_PYRAP PYRRH_PYRAP] Antibacterial peptide. Affects Gram-negative bacteria E.coli 1106, P.aeruginosa, E.coli D22 and E.cloacae and Gram-positive bacteria M.luteus and B.subtilis.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Acinetobacter baumannii d1279779]]
+[[Category: Acinetobacter baumannii D1279779]]
 [[Category: Large Structures]]
-[[Category: Harrop, S J]]
+[[Category: Harrop SJ]]
-[[Category: Mabbutt, B C]]
+[[Category: Mabbutt BC]]
-[[Category: Paulsen, I T]]
+[[Category: Paulsen IT]]
-[[Category: Shah, B S]]
+[[Category: Shah BS]]
-[[Category: Dehydratase]]
-[[Category: Isomerase]]
-[[Category: Nadp]]
-[[Category: Nucleoside-diphosphate sugar epimerase]]
-[[Category: Rossmann fold]]

4j2o

From Proteopedia

Revision as of 21:27, 16 November 2022

Crystal structure of NADP-bound WbjB from A. baumannii community strain D1279779

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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