3bss

From Proteopedia

(Difference between revisions)

Current revision

PglD from Campylobacter jejuni, NCTC 11168, with native substrate

Structural highlights

3bss is a 1 chain structure with sequence from Campylobacter jejuni. 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:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PGLD_CAMJE Acetyltransferase that modifies the UDP-4-amino-sugar to form UDP-N,N'-diacetylbacillosamine in the N-linked protein glycosylation pathway.^[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

The carbohydrate 2, 4-diacetamido-2, 4, 6-trideoxy-alpha-D-glucopyranose (BacAc(2)) is found in a variety of eubacterial pathogens. In Campylobacter jejuni, PglD acetylates the C4 amino group on UDP-2-acetamido-4-amino-2, 4, 6-trideoxy-alpha-D-glucopyranose (UDP-4-amino-sugar) to form UDP-BacAc(2). Sequence analysis predicts PglD to be a member of the left-handed beta helix family of enzymes. However, poor sequence homology between PglD and left-handed beta helix enzymes with existing structural data precludes unambiguous identification of the active site. The co-crystal structures of PglD in the presence of citrate, acetyl coenzyme A, or the UDP-4-amino-sugar were solved. The biological assembly is a trimer with one active site formed between two protomers. Residues lining the active site were identified, and results from functional assays on alanine mutants suggest His-125 is critical for catalysis, whereas His-15 and His-134 are involved in substrate binding. These results are discussed in the context of implications for proteins homologous to PglD in other pathogens.

Crystal structure and catalytic mechanism of PglD from Campylobacter jejuni.,Olivier NB, Imperiali B J Biol Chem. 2008 Oct 10;283(41):27937-46. Epub 2008 Jul 30. PMID:18667421^[3]

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

References

↑ Olivier NB, Chen MM, Behr JR, Imperiali B. In vitro biosynthesis of UDP-N,N'-diacetylbacillosamine by enzymes of the Campylobacter jejuni general protein glycosylation system. Biochemistry. 2006 Nov 14;45(45):13659-69. PMID:17087520 doi:http://dx.doi.org/10.1021/bi061456h
↑ Demendi M, Creuzenet C. Cj1123c (PglD), a multifaceted acetyltransferase from Campylobacter jejuni. Biochem Cell Biol. 2009 Jun;87(3):469-83. doi: 10.1139/o09-002. PMID:19448740 doi:http://dx.doi.org/10.1139/o09-002
↑ Olivier NB, Imperiali B. Crystal structure and catalytic mechanism of PglD from Campylobacter jejuni. J Biol Chem. 2008 Oct 10;283(41):27937-46. Epub 2008 Jul 30. PMID:18667421 doi:10.1074/jbc.M801207200

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/3bss"

Categories: Campylobacter jejuni | Large Structures | Imperiali B | Olivier NB

@@ Line 1: / Line 1: @@
 ==PglD from Campylobacter jejuni, NCTC 11168, with native substrate==
-<StructureSection load='3bss' size='340' side='right' caption='[[3bss]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='3bss' size='340' side='right'caption='[[3bss]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3bss]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_jejuni Campylobacter jejuni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BSS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BSS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3bss]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Campylobacter_jejuni Campylobacter jejuni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BSS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BSS FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UD4:UDP-2-ACETAMIDO-4-AMINO-2,4,6-TRIDEOXY-ALPHA-D-GLUCOPYRANOSE'>UD4</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2npo|2npo]], [[3bsw|3bsw]], [[3bsy|3bsy]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UD4:UDP-2-ACETAMIDO-4-AMINO-2,4,6-TRIDEOXY-ALPHA-D-GLUCOPYRANOSE'>UD4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pglD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197 Campylobacter jejuni])</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=3bss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bss OCA], [https://pdbe.org/3bss PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bss RCSB], [https://www.ebi.ac.uk/pdbsum/3bss PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bss ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylglucosamine_diphosphorylase UDP-N-acetylglucosamine diphosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.23 2.7.7.23] </span></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=3bss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bss OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bss RCSB], [http://www.ebi.ac.uk/pdbsum/3bss PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PGLD_CAMJE PGLD_CAMJE] Acetyltransferase that modifies the UDP-4-amino-sugar to form UDP-N,N'-diacetylbacillosamine in the N-linked protein glycosylation pathway.<ref>PMID:17087520</ref> <ref>PMID:19448740</ref>
 == 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/bs/3bss_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bs/3bss_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3bss ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3bss" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 32: / Line 34: @@
 </StructureSection>
 [[Category: Campylobacter jejuni]]
-[[Category: UDP-N-acetylglucosamine diphosphorylase]]
+[[Category: Large Structures]]
-[[Category: Imperiali, B.]]
+[[Category: Imperiali B]]
-[[Category: Olivier, N B.]]
+[[Category: Olivier NB]]
-[[Category: Acetyl coenzyme z]]
-[[Category: Bacillosamine]]
-[[Category: Campylobacter]]
-[[Category: Hexapeptide repeat]]
-[[Category: Left-hand beta helix]]
-[[Category: N-linked glycosylation]]
-[[Category: Pgl]]
-[[Category: Rossmann fold]]
-[[Category: Transferase]]
-[[Category: Udp]]

3bss

From Proteopedia

Current revision

PglD from Campylobacter jejuni, NCTC 11168, with native substrate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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