2bh2: Difference between revisions

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CRYSTAL STRUCTURE OF E. COLI 5-METHYLURIDINE METHYLTRANSFERASE RUMA IN COMPLEX WITH RIBOSOMAL RNA SUBSTRATE AND S-ADENOSYLHOMOCYSTEINE.

OverviewOverview

A single base (U1939) within E. coli 23S ribosomal RNA is methylated by its dedicated enzyme, RumA. The structure of RumA/RNA/S-adenosylhomocysteine uncovers the mechanism for achieving unique selectivity. The single-stranded substrate is "refolded" on the enzyme into a compact conformation with six key intra-RNA interactions. The RNA substrate contributes directly to catalysis. In addition to the target base, a second base is "flipped out" from the core loop to stack against the adenine of the cofactor S-adenosylhomocysteine. Nucleotides in permuted sequence order are stacked into the site vacated by the everted target U1939 and compensate for the energetic penalty of base eversion. The 3' hairpin segment of the RNA binds distal to the active site and provides binding energy that contributes to enhanced catalytic efficiency. Active collaboration of RNA in catalysis leads us to conclude that RumA and its substrate RNA may reflect features from the earliest RNA-protein era.

About this StructureAbout this Structure

2BH2 is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

ReferenceReference

A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function., Lee TT, Agarwalla S, Stroud RM, Cell. 2005 Mar 11;120(5):599-611. PMID:15766524

Page seeded by OCA on Thu Mar 20 16:01:54 2008

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:2bh2.gif|left|200px]]<br /><applet load="2bh2" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:2bh2.gif|left|200px]]
-caption="2bh2, resolution 2.15&Aring;" />
-'''CRYSTAL STRUCTURE OF E. COLI 5-METHYLURIDINE METHYLTRANSFERASE RUMA IN COMPLEX WITH RIBOSOMAL RNA SUBSTRATE AND S-ADENOSYLHOMOCYSTEINE.'''<br />
+ {{Structure
+|PDB= 2bh2 |SIZE=350|CAPTION= <scene name='initialview01'>2bh2</scene>, resolution 2.15&Aring;
+|SITE= <scene name='pdbsite=AC1:Fmu+Binding+Site+For+Chain+D'>AC1</scene>
+|LIGAND= <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene> and <scene name='pdbligand=SF4:IRON/SULFUR CLUSTER'>SF4</scene>
+|ACTIVITY=
+|GENE=
+}}
+'''CRYSTAL STRUCTURE OF E. COLI 5-METHYLURIDINE METHYLTRANSFERASE RUMA IN COMPLEX WITH RIBOSOMAL RNA SUBSTRATE AND S-ADENOSYLHOMOCYSTEINE.'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-BH2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=SAH:'>SAH</scene> and <scene name='pdbligand=SF4:'>SF4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Site: <scene name='pdbsite=AC1:Fmu+Binding+Site+For+Chain+D'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BH2 OCA].
+BH2 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BH2 OCA].
 ==Reference==
-A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function., Lee TT, Agarwalla S, Stroud RM, Cell. 2005 Mar 11;120(5):599-611. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15766524 15766524]
+A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function., Lee TT, Agarwalla S, Stroud RM, Cell. 2005 Mar 11;120(5):599-611. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15766524 15766524]
 [[Category: Escherichia coli]]
 [[Category: Single protein]]
@@ Line 18: / Line 27: @@
 [[Category: SAH]]
 [[Category: SF4]]
-[[Category: 4fe-4s]]
+[[Category: 4fe-4]]
 [[Category: base flipping]]
 [[Category: base stacking]]
@@ Line 36: / Line 45: @@
 [[Category: transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:37:45 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:01:54 2008''