1pvw

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1pvw" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pvw, resolution 2.45&Aring;" /> '''3,4-dihydroxy-2-buta...)
Current revision (13:28, 13 March 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1pvw.jpg|left|200px]]<br /><applet load="1pvw" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1pvw, resolution 2.45&Aring;" />
 
-
'''3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii'''<br />
 
-
==Overview==
+
==3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii==
-
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.
+
<StructureSection load='1pvw' size='340' side='right'caption='[[1pvw]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1pvw]] is a 3 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=1PVW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PVW FirstGlance]. <br>
-
1PVW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii] with ZN, CA and PO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PVW OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.45&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pvw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvw OCA], [https://pdbe.org/1pvw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pvw RCSB], [https://www.ebi.ac.uk/pdbsum/1pvw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pvw ProSAT]</span></td></tr>
-
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12904291 12904291]
+
</table>
 +
== Function ==
 +
[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/1pvw_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/main_output.php?pdb_ID=1pvw ConSurf].
 +
<div style="clear:both"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]
-
[[Category: Single protein]]
+
[[Category: Bacher A]]
-
[[Category: Bacher, A.]]
+
[[Category: Fischer M]]
-
[[Category: Fischer, M.]]
+
[[Category: Huber R]]
-
[[Category: Huber, R.]]
+
[[Category: Richter G]]
-
[[Category: Richter, G.]]
+
[[Category: Schiffmann S]]
-
[[Category: Schiffmann, S.]]
+
[[Category: Steinbacher S]]
-
[[Category: Steinbacher, S.]]
+
-
[[Category: CA]]
+
-
[[Category: PO4]]
+
-
[[Category: ZN]]
+
-
[[Category: riboflavin biosynthesis]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:10:10 2007''
+

Current revision

3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii

PDB ID 1pvw

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1pvw"
Personal tools