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3dr7

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GDP-perosamine synthase from Caulobacter crescentus with bound GDP-3-deoxyperosamine

Structural highlights

3dr7 is a 4 chain structure with sequence from Caulobacter vibrioides CB15. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GDPPS_CAUVC Catalyzes the synthesis of GDP-perosamine from GDP-4-keto-6-deoxy-D-mannose and L-glutamate. Can use only L-glutamate as amino donor. In vitro, can also use GDP-4-keto-3,6-dideoxymannose to produce GDP-3-deoxyperosamine. Involved in the formation of S-LPS, which is required for attachment of the protein S-layer to the outer membrane surface.^[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

Perosamine (4-amino-4,6-dideoxy- d-mannose), or its N-acetylated form, is one of several dideoxy sugars found in the O-antigens of such infamous Gram-negative bacteria as Vibrio cholerae O1 and Escherichia coli O157:H7. It is added to the bacterial O-antigen via a nucleotide-linked version, namely GDP-perosamine. Three enzymes are required for the biosynthesis of GDP-perosamine starting from mannose 1-phosphate. The focus of this investigation is GDP-perosamine synthase from Caulobacter crescentus, which catalyzes the final step in GDP-perosamine synthesis, the conversion of GDP-4-keto-6-deoxymannose to GDP-perosamine. The enzyme is PLP-dependent and belongs to the aspartate aminotransferase superfamily. It contains the typically conserved active site lysine residue, which forms a Schiff base with the PLP cofactor. Two crystal structures were determined for this investigation: a site-directed mutant protein (K186A) complexed with GDP-perosamine and the wild-type enzyme complexed with an unnatural ligand, GDP-3-deoxyperosamine. These structures, determined to 1.6 and 1.7 A resolution, respectively, revealed the manner in which products, and presumably substrates, are accommodated within the active site pocket of GDP-perosamine synthase. Additional kinetic analyses using both the natural and unnatural substrates revealed that the K m for the unnatural substrate was unperturbed relative to that of the natural substrate, but the k cat was lowered by a factor of approximately 200. Taken together, these studies shed light on why GDP-perosamine synthase functions as an aminotransferase whereas another very similar PLP-dependent enzyme, GDP-4-keto-6-deoxy- d-mannose 3-dehydratase or ColD, catalyzes a dehydration reaction using the same substrate.

Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase.,Cook PD, Carney AE, Holden HM Biochemistry. 2008 Oct 7;47(40):10685-93. Epub 2008 Sep 17. PMID:18795799^[4]

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

References

↑ Awram P, Smit J. Identification of lipopolysaccharide O antigen synthesis genes required for attachment of the S-layer of Caulobacter crescentus. Microbiology. 2001 Jun;147(Pt 6):1451-60. PMID:11390676
↑ Cook PD, Holden HM. GDP-Perosamine Synthase: Structural Analysis and Production of a Novel Trideoxysugar(,). Biochemistry. 2008 Mar 4;47(9):2833-40. Epub 2008 Feb 5. PMID:18247575 doi:10.1021/bi702430d
↑ Cook PD, Carney AE, Holden HM. Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase. Biochemistry. 2008 Oct 7;47(40):10685-93. Epub 2008 Sep 17. PMID:18795799 doi:10.1021/bi801309q
↑ Cook PD, Carney AE, Holden HM. Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase. Biochemistry. 2008 Oct 7;47(40):10685-93. Epub 2008 Sep 17. PMID:18795799 doi:10.1021/bi801309q

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/3dr7"

Categories: Caulobacter vibrioides CB15 | Large Structures | Carney AE | Cook PD | Holden HM

@@ Line 1: / Line 1: @@
 ==GDP-perosamine synthase from Caulobacter crescentus with bound GDP-3-deoxyperosamine==
-<StructureSection load='3dr7' size='340' side='right' caption='[[3dr7]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+<StructureSection load='3dr7' size='340' side='right'caption='[[3dr7]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3dr7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DR7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3dr7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides_CB15 Caulobacter vibrioides CB15]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DR7 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GPD:(2R,3S,5S,6R)-5-AMINO-3-HYDROXY-6-METHYL-OXAN-2-YL'>GPD</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]] 1.7&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GPD:(2R,3S,5S,6R)-5-AMINO-3-HYDROXY-6-METHYL-OXAN-2-YL'>GPD</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3bn1|3bn1]], [[3dr4|3dr4]]</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=3dr7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dr7 OCA], [https://pdbe.org/3dr7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dr7 RCSB], [https://www.ebi.ac.uk/pdbsum/3dr7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dr7 ProSAT]</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=3dr7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dr7 OCA], [http://pdbe.org/3dr7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dr7 RCSB], [http://www.ebi.ac.uk/pdbsum/3dr7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dr7 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/O85354_CAUCE O85354_CAUCE]] Catalyzes the synthesis of GDP-perosamine from GDP-4-keto-6-deoxy-D-mannose and L-glutamate. Can use only L-glutamate as amino donor. In vitro, can also use GDP-4-keto-3,6-dideoxymannose to produce GDP-3-deoxyperosamine. Involved in the formation of S-LPS, which is required for attachment of the protein S-layer to the outer membrane surface.<ref>PMID:11390676</ref> <ref>PMID:18247575</ref> <ref>PMID:18795799</ref>
+[https://www.uniprot.org/uniprot/GDPPS_CAUVC GDPPS_CAUVC] Catalyzes the synthesis of GDP-perosamine from GDP-4-keto-6-deoxy-D-mannose and L-glutamate. Can use only L-glutamate as amino donor. In vitro, can also use GDP-4-keto-3,6-dideoxymannose to produce GDP-3-deoxyperosamine. Involved in the formation of S-LPS, which is required for attachment of the protein S-layer to the outer membrane surface.<ref>PMID:11390676</ref> <ref>PMID:18247575</ref> <ref>PMID:18795799</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/dr/3dr7_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dr/3dr7_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 34: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Carney, A E]]
+[[Category: Caulobacter vibrioides CB15]]
-[[Category: Cook, P D]]
+[[Category: Large Structures]]
-[[Category: Holden, H M]]
+[[Category: Carney AE]]
-[[Category: Aspartate aminotransferase]]
+[[Category: Cook PD]]
-[[Category: Deoxysugar]]
+[[Category: Holden HM]]
-[[Category: Lipopolysaccharide]]
-[[Category: O-antigen]]
-[[Category: Perosamine]]
-[[Category: Pyridoxal phosphate]]
-[[Category: Transferase]]

3dr7

From Proteopedia

Current revision

GDP-perosamine synthase from Caulobacter crescentus with bound GDP-3-deoxyperosamine

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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