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3dr4

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GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand

Structural highlights

3dr4 is a 4 chain structure with sequence from Caulobacter vibrioides. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.6Å
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/3dr4"

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

@@ Line 1: / Line 1: @@
 ==GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand==
-<StructureSection load='3dr4' size='340' side='right' caption='[[3dr4]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='3dr4' size='340' side='right'caption='[[3dr4]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3dr4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DR4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3dr4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DR4 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=G4M:[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+(2R,3S,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL+DIHYDROGEN+DIPHOSPHATE'>G4M</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]] 1.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3bn1|3bn1]], [[3dr7|3dr7]]</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=G4M:[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+(2R,3S,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL+DIHYDROGEN+DIPHOSPHATE'>G4M</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">per ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155892 Caulobacter vibrioides])</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=3dr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dr4 OCA], [https://pdbe.org/3dr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dr4 RCSB], [https://www.ebi.ac.uk/pdbsum/3dr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dr4 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=3dr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dr4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dr4 RCSB], [http://www.ebi.ac.uk/pdbsum/3dr4 PDBsum]</span></td></tr>
 </table>
+== Function ==
+[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/3dr4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dr/3dr4_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=3dr4 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3dr4" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 31: / Line 34: @@
 </StructureSection>
 [[Category: Caulobacter vibrioides]]
-[[Category: Carney, A E]]
+[[Category: Large Structures]]
-[[Category: Cook, P D]]
+[[Category: Carney AE]]
-[[Category: Holden, H M]]
+[[Category: Cook PD]]
-[[Category: Aspartate aminotransferase]]
+[[Category: Holden HM]]
-[[Category: Deoxysugar]]
-[[Category: O-antigen]]
-[[Category: Perosamine]]
-[[Category: Pyridoxal phosphate]]
-[[Category: Transferase]]

3dr4

From Proteopedia

Current revision

GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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