3gee

From Proteopedia

(Difference between revisions)

Revision as of 05:23, 5 August 2016

Crystal structure of MnmE from Chlorobium tepidum in complex with GDP and FOLINIC ACID

Structural highlights

3gee is a 1 chain structure with sequence from Atcc 49652. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1rfl, 1xzp, 1xzq, 2gja, 2gj8, 2gj9, 3cp2, 3cp8, 3geh, 3gei
Gene:	mnmE, CT2084, thdF, trmE (ATCC 49652)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[MNME_CHLTE] Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34.[HAMAP-Rule:MF_00379]

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

MnmE, which is involved in the modification of the wobble position of certain tRNAs, belongs to the expanding class of G proteins activated by nucleotide-dependent dimerization (GADs). Previous models suggested the protein to be a multidomain protein whose G domains contact each other in a nucleotide dependent manner. Here we employ a combined approach of X-ray crystallography and pulse electron paramagnetic resonance (EPR) spectroscopy to show that large domain movements are coupled to the G protein cycle of MnmE. The X-ray structures show MnmE to be a constitutive homodimer where the highly mobile G domains face each other in various orientations but are not in close contact as suggested by the GDP-AlF(x) structure of the isolated domains. Distance measurements by pulse double electron-electron resonance (DEER) spectroscopy show that the G domains adopt an open conformation in the nucleotide free/GDP-bound and an open/closed two-state equilibrium in the GTP-bound state, with maximal distance variations of 18 A. With GDP and AlF(x), which mimic the transition state of the phosphoryl transfer reaction, only the closed conformation is observed. Dimerization of the active sites with GDP-AlF(x) requires the presence of specific monovalent cations, thus reflecting the requirements for the GTPase reaction of MnmE. Our results directly demonstrate the nature of the conformational changes MnmE was previously suggested to undergo during its GTPase cycle. They show the nucleotide-dependent dynamic movements of the G domains around two swivel positions relative to the rest of the protein, and they are of crucial importance for understanding the mechanistic principles of this GAD.

Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy.,Meyer S, Bohme S, Kruger A, Steinhoff HJ, Klare JP, Wittinghofer A PLoS Biol. 2009 Oct;7(10):e1000212. Epub 2009 Oct 6. PMID:19806182^[1]

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

References

↑ Meyer S, Bohme S, Kruger A, Steinhoff HJ, Klare JP, Wittinghofer A. Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy. PLoS Biol. 2009 Oct;7(10):e1000212. Epub 2009 Oct 6. PMID:19806182 doi:10.1371/journal.pbio.1000212

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/3gee"

@@ Line 1: / Line 1: @@
 ==Crystal structure of MnmE from Chlorobium tepidum in complex with GDP and FOLINIC ACID==
 <StructureSection load='3gee' size='340' side='right' caption='[[3gee]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3gee]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chlorobaculum_tepidum Chlorobaculum tepidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GEE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GEE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3gee]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_49652 Atcc 49652]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GEE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GEE FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FON:N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC+ACID'>FON</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1rfl|1rfl]], [[1xzp|1xzp]], [[1xzq|1xzq]], [[2gja|2gja]], [[2gj8|2gj8]], [[2gj9|2gj9]], [[3cp2|3cp2]], [[3cp8|3cp8]], [[3geh|3geh]], [[3gei|3gei]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mnmE, CT2084, thdF, trmE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1097 Chlorobaculum tepidum])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mnmE, CT2084, thdF, trmE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1097 ATCC 49652])</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=3gee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gee OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gee RCSB], [http://www.ebi.ac.uk/pdbsum/3gee PDBsum]</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=3gee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gee OCA], [http://pdbe.org/3gee PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gee RCSB], [http://www.ebi.ac.uk/pdbsum/3gee PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gee ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 19: @@
     <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=3gee ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3gee" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Chlorobaculum tepidum]]
+[[Category: Atcc 49652]]
 [[Category: Meyer, S]]
 [[Category: Wittinghofer, A]]

3gee

From Proteopedia

Revision as of 05:23, 5 August 2016

Crystal structure of MnmE from Chlorobium tepidum in complex with GDP and FOLINIC ACID

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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