2vdc

From Proteopedia

(Difference between revisions)

Current revision

THE 9.5 A RESOLUTION STRUCTURE OF GLUTAMATE SYNTHASE FROM CRYO-ELECTRON MICROSCOPY AND ITS OLIGOMERIZATION BEHAVIOR IN SOLUTION: FUNCTIONAL IMPLICATIONS.

2vdc, resolution 9.50Å

Structural highlights

2vdc is a 12 chain structure with sequence from Azospirillum brasilense. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 9.5Å
Ligands:
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GLTB_AZOBR

Evolutionary Conservation

Checkto colour the structure by Evolutionary Conservation, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The three-dimensional structure of the hexameric (alphabeta)(6) 1.2-MDa complex formed by glutamate synthase has been determined at subnanometric resolution by combining cryoelectron microscopy, small angle x-ray scattering, and molecular modeling, providing for the first time a molecular model of this complex iron-sulfur flavoprotein. In the hexameric species, interprotomeric alpha-alpha and alpha-beta contacts are mediated by the C-terminal domain of the alpha subunit, which is based on a beta helical fold so far unique to glutamate synthases. The alphabeta protomer extracted from the hexameric model is fully consistent with it being the minimal catalytically active form of the enzyme. The structure clarifies the electron transfer pathway from the FAD cofactor on the beta subunit, to the FMN on the alpha subunit, through the low potential [4Fe-4S](1+/2+) centers on the beta subunit and the [3Fe-4S](0/1+) cluster on the alpha subunit. The (alphabeta)(6) hexamer exhibits a concentration-dependent equilibrium with alphabeta monomers and (alphabeta)(2) dimers, in solution, the hexamer being destabilized by high ionic strength and, to a lower extent, by the reaction product NADP(+). Hexamerization seems to decrease the catalytic efficiency of the alphabeta protomer only 3-fold by increasing the K(m) values measured for l-Gln and 2-OG. However, it cannot be ruled out that the (alphabeta)(6) hexamer acts as a scaffold for the assembly of multienzymatic complexes of nitrogen metabolism or that it provides a means to regulate the activity of the enzyme through an as yet unknown ligand.

The subnanometer resolution structure of the glutamate synthase 1.2-MDa hexamer by cryoelectron microscopy and its oligomerization behavior in solution: functional implications.,Cottevieille M, Larquet E, Jonic S, Petoukhov MV, Caprini G, Paravisi S, Svergun DI, Vanoni MA, Boisset N J Biol Chem. 2008 Mar 28;283(13):8237-49. Epub 2008 Jan 16. PMID:18199747^[1]

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

References

↑ Cottevieille M, Larquet E, Jonic S, Petoukhov MV, Caprini G, Paravisi S, Svergun DI, Vanoni MA, Boisset N. The subnanometer resolution structure of the glutamate synthase 1.2-MDa hexamer by cryoelectron microscopy and its oligomerization behavior in solution: functional implications. J Biol Chem. 2008 Mar 28;283(13):8237-49. Epub 2008 Jan 16. PMID:18199747 doi:10.1074/jbc.M708529200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2vdc"

@@ Line 1: / Line 1: @@
-{{Large structure}}
 ==THE 9.5 A RESOLUTION STRUCTURE OF GLUTAMATE SYNTHASE FROM CRYO-ELECTRON MICROSCOPY AND ITS OLIGOMERIZATION BEHAVIOR IN SOLUTION: FUNCTIONAL IMPLICATIONS.==
-<StructureSection load='2vdc' size='340' side='right' caption='[[2vdc]], [[Resolution|resolution]] 9.50&Aring;' scene=''>
+<SX load='2vdc' size='340' side='right' viewer='molstar' caption='[[2vdc]], [[Resolution|resolution]] 9.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vdc]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29145 Atcc 29145]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VDC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vdc]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Azospirillum_brasilense Azospirillum brasilense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VDC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=OMT:S-DIOXYMETHIONINE'>OMT</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 9.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ea0|1ea0]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=OMT:S-DIOXYMETHIONINE'>OMT</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate_synthase_(NADPH) Glutamate synthase (NADPH)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.13 1.4.1.13] </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=2vdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vdc OCA], [https://pdbe.org/2vdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vdc RCSB], [https://www.ebi.ac.uk/pdbsum/2vdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vdc 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=2vdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vdc OCA], [http://pdbe.org/2vdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vdc RCSB], [http://www.ebi.ac.uk/pdbsum/2vdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vdc ProSAT]</span></td></tr>
 </table>
-{{Large structure}}
+== Function ==
+[https://www.uniprot.org/uniprot/GLTB_AZOBR GLTB_AZOBR]
 == 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/vd/2vdc_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vd/2vdc_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 2vdc" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Glutamate synthase|Glutamate synthase]]
 == References ==
 <references/>
 __TOC__
-</StructureSection>
+</SX>
-[[Category: Atcc 29145]]
+[[Category: Azospirillum brasilense]]
-[[Category: Boisset, N]]
+[[Category: Large Structures]]
-[[Category: Caprini, G]]
+[[Category: Boisset N]]
-[[Category: Cottevieille, M]]
+[[Category: Caprini G]]
-[[Category: Jonic, S]]
+[[Category: Cottevieille M]]
-[[Category: Larquet, E]]
+[[Category: Jonic S]]
-[[Category: Paravisi, S]]
+[[Category: Larquet E]]
-[[Category: Petoukhov, M V]]
+[[Category: Paravisi S]]
-[[Category: Svergun, D I]]
+[[Category: Petoukhov MV]]
-[[Category: Vanoni, M A]]
+[[Category: Svergun DI]]
-[[Category: Amidotransferase]]
+[[Category: Vanoni MA]]
-[[Category: Amino-acid biosynthesis]]
-[[Category: Ammonia assimilation]]
-[[Category: Glutamate biosynthesis]]
-[[Category: Glutamine amidotransferase]]
-[[Category: Iron]]
-[[Category: Iron sulphur flavoprotein]]
-[[Category: Nadp]]
-[[Category: Nadph-dependent glutamate synthase]]
-[[Category: Oxidoreductase]]
-[[Category: Zymogen]]

2vdc

From Proteopedia

Current revision

THE 9.5 A RESOLUTION STRUCTURE OF GLUTAMATE SYNTHASE FROM CRYO-ELECTRON MICROSCOPY AND ITS OLIGOMERIZATION BEHAVIOR IN SOLUTION: FUNCTIONAL IMPLICATIONS.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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