1wb3: Difference between revisions

← Older edit Newer edit →

Revision as of 15:54, 20 March 2008

File:1wb3.gif

, resolution 3.20Å

Sites:

Ligands:

, , and

Coordinates:

save as pdb, mmCIF, xml

CRYSTAL STRUCTURE OF TRANSLATION ELONGATION FACTOR SELB FROM METHANOCOCCUS MARIPALUDIS IN COMPLEX WITH THE GTP ANALOGUE GPPNHP

OverviewOverview

In all three kingdoms of life, SelB is a specialized translation elongation factor responsible for the cotranslational incorporation of selenocysteine into proteins by recoding of a UGA stop codon in the presence of a downstream mRNA hairpin loop. Here, we present the X-ray structures of SelB from the archaeon Methanococcus maripaludis in the apo-, GDP- and GppNHp-bound form and use mutational analysis to investigate the role of individual amino acids in its aminoacyl-binding pocket. All three SelB structures reveal an EF-Tu:GTP-like domain arrangement. Upon binding of the GTP analogue GppNHp, a conformational change of the Switch 2 region in the GTPase domain leads to the exposure of SelB residues involved in clamping the 5' phosphate of the tRNA. A conserved extended loop in domain III of SelB may be responsible for specific interactions with tRNA(Sec) and act as a ruler for measuring the extra long acceptor arm. Domain IV of SelB adopts a beta barrel fold and is flexibly tethered to domain III. The overall domain arrangement of SelB resembles a 'chalice' observed so far only for initiation factor IF2/eIF5B. In our model of SelB bound to the ribosome, domain IV points towards the 3' mRNA entrance cleft ready to interact with the downstream secondary structure element.

About this StructureAbout this Structure

1WB3 is a Single protein structure of sequence from Methanococcus maripaludis. Full crystallographic information is available from OCA.

ReferenceReference

Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors., Leibundgut M, Frick C, Thanbichler M, Bock A, Ban N, EMBO J. 2005 Jan 12;24(1):11-22. Epub 2004 Dec 23. PMID:15616587

Page seeded by OCA on Thu Mar 20 14:54:36 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1wb3.gif|left|200px]]<br /><applet load="1wb3" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:1wb3.gif|left|200px]]
-caption="1wb3, resolution 3.20&Aring;" />
-'''CRYSTAL STRUCTURE OF TRANSLATION ELONGATION FACTOR SELB FROM METHANOCOCCUS MARIPALUDIS IN COMPLEX WITH THE GTP ANALOGUE GPPNHP'''<br />
+ {{Structure
+|PDB= 1wb3 |SIZE=350|CAPTION= <scene name='initialview01'>1wb3</scene>, resolution 3.20&Aring;
+|SITE= <scene name='pdbsite=AC1:Dxc+Binding+Site+For+Chain+C'>AC1</scene>
+|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene> and <scene name='pdbligand=DXC:(3ALPHA,5ALPHA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID'>DXC</scene>
+|ACTIVITY=
+|GENE=
+}}
+'''CRYSTAL STRUCTURE OF TRANSLATION ELONGATION FACTOR SELB FROM METHANOCOCCUS MARIPALUDIS IN COMPLEX WITH THE GTP ANALOGUE GPPNHP'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-WB3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanococcus_maripaludis Methanococcus maripaludis] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=GNP:'>GNP</scene> and <scene name='pdbligand=DXC:'>DXC</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Site: <scene name='pdbsite=AC1:Dxc+Binding+Site+For+Chain+C'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WB3 OCA].
+WB3 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanococcus_maripaludis Methanococcus maripaludis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WB3 OCA].
 ==Reference==
-Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors., Leibundgut M, Frick C, Thanbichler M, Bock A, Ban N, EMBO J. 2005 Jan 12;24(1):11-22. Epub 2004 Dec 23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15616587 15616587]
+Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors., Leibundgut M, Frick C, Thanbichler M, Bock A, Ban N, EMBO J. 2005 Jan 12;24(1):11-22. Epub 2004 Dec 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15616587 15616587]
 [[Category: Methanococcus maripaludis]]
 [[Category: Single protein]]
@@ Line 27: / Line 36: @@
 [[Category: selenocysteine]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:42:21 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:54:36 2008''