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1pvy

From Proteopedia

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3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii in complex with ribulose 5-phosphate

Structural highlights

1pvy is a 2 chain structure with sequence from Methanocaldococcus jannaschii. 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

RIBB_METJA Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.^[1]

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

Skeletal rearrangements of carbohydrates are crucial for many biosynthetic pathways. In riboflavin biosynthesis ribulose 5-phosphate is converted into 3,4-dihydroxy-2-butanone 4-phosphate while its C4 atom is released as formate in a sequence of metal-dependent reactions. Here, we present the crystal structure of Methanococcus jannaschii 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with the substrate ribulose 5-phosphate at a dimetal center presumably consisting of non-catalytic zinc and calcium ions at 1.7-A resolution. The carbonyl group (O2) and two out of three free hydroxyl groups (OH3 and OH4) of the substrate are metal-coordinated. We correlate previous mutational studies on this enzyme with the present structural results. Residues of the first coordination sphere involved in metal binding are indispensable for catalytic activity. Only Glu-185 of the second coordination sphere cannot be replaced without complete loss of activity. It contacts the C3 hydrogen atom directly and probably initiates enediol formation in concert with both metal ions to start the reaction sequence. Mechanistic similarities to Rubisco acting on the similar substrate ribulose 1,5-diphosphate in carbon dioxide fixation as well as other carbohydrate (reducto-) isomerases are discussed.

Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism.,Steinbacher S, Schiffmann S, Richter G, Huber R, Bacher A, Fischer M J Biol Chem. 2003 Oct 24;278(43):42256-65. Epub 2003 Aug 6. PMID:12904291^[2]

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

References

↑ Fischer M, Romisch W, Schiffmann S, Kelly M, Oschkinat H, Steinbacher S, Huber R, Eisenreich W, Richter G, Bacher A. Biosynthesis of riboflavin in archaea studies on the mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase of Methanococcus jannaschii. J Biol Chem. 2002 Nov 1;277(44):41410-6. Epub 2002 Aug 27. PMID:12200440 doi:http://dx.doi.org/10.1074/jbc.M206863200
↑ Steinbacher S, Schiffmann S, Richter G, Huber R, Bacher A, Fischer M. Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism. J Biol Chem. 2003 Oct 24;278(43):42256-65. Epub 2003 Aug 6. PMID:12904291 doi:http://dx.doi.org/10.1074/jbc.M307301200

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/1pvy"

@@ Line 1: / Line 1: @@
 ==3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii in complex with ribulose 5-phosphate==
-<StructureSection load='1pvy' size='340' side='right' caption='[[1pvy]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+<StructureSection load='1pvy' size='340' side='right'caption='[[1pvy]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1pvy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PVY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1pvy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PVY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5RP:RIBULOSE-5-PHOSPHATE'>5RP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1pvw|1pvw]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5RP:RIBULOSE-5-PHOSPHATE'>5RP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MJ0055 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=1pvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvy OCA], [https://pdbe.org/1pvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pvy RCSB], [https://www.ebi.ac.uk/pdbsum/1pvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pvy 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=1pvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvy OCA], [http://pdbe.org/1pvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pvy RCSB], [http://www.ebi.ac.uk/pdbsum/1pvy PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RIBB_METJA RIBB_METJA]] Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.<ref>PMID:12200440</ref>
+[https://www.uniprot.org/uniprot/RIBB_METJA RIBB_METJA] Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.<ref>PMID:12200440</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/pv/1pvy_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pv/1pvy_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=1pvy ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 43067]]
+[[Category: Large Structures]]
-[[Category: Bacher, A]]
+[[Category: Methanocaldococcus jannaschii]]
-[[Category: Fischer, M]]
+[[Category: Bacher A]]
-[[Category: Huber, R]]
+[[Category: Fischer M]]
-[[Category: Richter, G]]
+[[Category: Huber R]]
-[[Category: Schiffmann, S]]
+[[Category: Richter G]]
-[[Category: Steinbacher, S]]
+[[Category: Schiffmann S]]
-[[Category: Isomerase]]
+[[Category: Steinbacher S]]
-[[Category: Riboflavin biosynthesis]]

1pvy

From Proteopedia

Current revision

3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii in complex with ribulose 5-phosphate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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