2pk3

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of a GDP-4-keto-6-deoxy-D-mannose reductase

Structural highlights

2pk3 is a 2 chain structure with sequence from Aneurinibacillus thermoaerophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.82Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RMD_ANETH Reductase that catalyzes the conversion of GDP-6-deoxy-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose (GDP-D-rhamnose).^[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 rare 6-deoxysugar D-rhamnose is a component of bacterial cell surface glycans, including the D-rhamnose homopolymer produced by Pseudomonas aeruginosa, called A-band O polysaccharide. GDP-D-rhamnose synthesis from GDP-D-mannose is catalyzed by two enzymes. The first is a GDP-D-mannose-4,6-dehydratase (GMD). The second enzyme, RMD, reduces the GMD product (GDP-6-deoxy-D-lyxo-hexos-4-ulose) to GDP-d-rhamnose. Genes encoding GMD and RMD are present in P. aeruginosa, and genetic evidence indicates they act in A-band O-polysaccharide biosynthesis. Details of their enzyme functions have not, however, been previously elucidated. We aimed to characterize these enzymes biochemically, and to determine the structure of RMD to better understand what determines substrate specificity and catalytic activity in these enzymes. We used capillary electrophoresis and NMR analysis of reaction products to precisely define P. aeruginosa GMD and RMD functions. P. aeruginosa GMD is bifunctional, and can catalyze both GDP-d-mannose 4,6-dehydration and the subsequent reduction reaction to produce GDP-D-rhamnose. RMD catalyzes the stereospecific reduction of GDP-6-deoxy-D-lyxo-hexos-4-ulose, as predicted. Reconstitution of GDP-D-rhamnose biosynthesis in vitro revealed that the P. aeruginosa pathway may be regulated by feedback inhibition in the cell. We determined the structure of RMD from Aneurinibacillus thermoaerophilus at 1.8 A resolution. The structure of A. thermoaerophilus RMD is remarkably similar to that of P. aeruginosa GMD, which explains why P. aeruginosa GMD is also able to catalyze the RMD reaction. Comparison of the active sites and amino acid sequences suggests that a conserved amino acid side chain (Arg185 in P. aeruginosa GMD) may be crucial for orienting substrate and cofactor in GMD enzymes.

The structural basis for catalytic function of GMD and RMD, two closely related enzymes from the GDP-D-rhamnose biosynthesis pathway.,King JD, Poon KK, Webb NA, Anderson EM, McNally DJ, Brisson JR, Messner P, Garavito RM, Lam JS FEBS J. 2009 May;276(10):2686-700. PMID:19459932^[3]

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

References

↑ Kneidinger B, Graninger M, Adam G, Puchberger M, Kosma P, Zayni S, Messner P. Identification of two GDP-6-deoxy-D-lyxo-4-hexulose reductases synthesizing GDP-D-rhamnose in Aneurinibacillus thermoaerophilus L420-91T. J Biol Chem. 2001 Feb 23;276(8):5577-83. Epub 2000 Nov 28. PMID:11096116 doi:http://dx.doi.org/10.1074/jbc.M010027200
↑ King JD, Poon KK, Webb NA, Anderson EM, McNally DJ, Brisson JR, Messner P, Garavito RM, Lam JS. The structural basis for catalytic function of GMD and RMD, two closely related enzymes from the GDP-D-rhamnose biosynthesis pathway. FEBS J. 2009 May;276(10):2686-700. PMID:19459932 doi:10.1111/j.1742-4658.2009.06993.x
↑ King JD, Poon KK, Webb NA, Anderson EM, McNally DJ, Brisson JR, Messner P, Garavito RM, Lam JS. The structural basis for catalytic function of GMD and RMD, two closely related enzymes from the GDP-D-rhamnose biosynthesis pathway. FEBS J. 2009 May;276(10):2686-700. PMID:19459932 doi:10.1111/j.1742-4658.2009.06993.x

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/2pk3"

Categories: Aneurinibacillus thermoaerophilus | Large Structures | Garavito RM | Webb NA

@@ Line 1: / Line 1: @@
 ==Crystal Structure of a GDP-4-keto-6-deoxy-D-mannose reductase==
-<StructureSection load='2pk3' size='340' side='right' caption='[[2pk3]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
+<StructureSection load='2pk3' size='340' side='right'caption='[[2pk3]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2pk3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aneth Aneth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PK3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PK3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2pk3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aneurinibacillus_thermoaerophilus Aneurinibacillus thermoaerophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PK3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PK3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2R:[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL+[(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>A2R</scene>, <scene name='pdbligand=GDD:GUANOSINE-5-DIPHOSPHATE-ALPHA-D-MANNOSE'>GDD</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]] 1.82&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rmd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=143495 ANETH])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2R:[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL+[(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>A2R</scene>, <scene name='pdbligand=GDD:GUANOSINE-5-DIPHOSPHATE-ALPHA-D-MANNOSE'>GDD</scene></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=2pk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pk3 OCA], [http://pdbe.org/2pk3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pk3 RCSB], [http://www.ebi.ac.uk/pdbsum/2pk3 PDBsum]</span></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=2pk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pk3 OCA], [https://pdbe.org/2pk3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pk3 RCSB], [https://www.ebi.ac.uk/pdbsum/2pk3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pk3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RMD_ANETH RMD_ANETH]] Reductase that catalyzes the conversion of GDP-6-deoxy-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose (GDP-D-rhamnose).<ref>PMID:11096116</ref> <ref>PMID:19459932</ref>
+[https://www.uniprot.org/uniprot/RMD_ANETH RMD_ANETH] Reductase that catalyzes the conversion of GDP-6-deoxy-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose (GDP-D-rhamnose).<ref>PMID:11096116</ref> <ref>PMID:19459932</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/pk/2pk3_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pk/2pk3_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=2pk3 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Aneth]]
+[[Category: Aneurinibacillus thermoaerophilus]]
-[[Category: Garavito, R M]]
+[[Category: Large Structures]]
-[[Category: Webb, N A]]
+[[Category: Garavito RM]]
-[[Category: Oxidoreductase]]
+[[Category: Webb NA]]
-[[Category: Rossmann fold]]
-[[Category: Sdr]]
-[[Category: Short-chain dehydrogenase/reductase]]

2pk3

From Proteopedia

Current revision

Crystal Structure of a GDP-4-keto-6-deoxy-D-mannose reductase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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