3c3d: Difference between revisions

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Revision as of 20:02, 20 March 2008

File:3c3d.jpg

, resolution 2.50Å

Sites:

, , , , , , and

Ligands:

and

Gene:

cofD, MM_1874 (Methanosarcina mazei Go1)

Coordinates:

save as pdb, mmCIF, xml

Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and phosphate. Northeast Structural Genomics Consortium target MaR46

OverviewOverview

Coenzyme F420, a hydride carrier, is found in archaea and some bacteria and has crucial roles in methanogenesis, antibiotics biosynthesis, DNA repair, and activation of antitubercular compounds. CofD, 2-phospho-L-lactate transferase, catalyzes the last step in the biosynthesis of F420-0 (F420 without polyglutamate), by transferring the lactyl phosphate (LP) moiety of lactyl (2) diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (Fo). CofD is highly conserved among F420-producing organisms, and weak sequence homologs are also found in non-F420-producing organisms. This superfamily does not share any recognizable sequence conservation with other proteins. Here we report the first crystal structures of CofD-the free enzyme and two ternary complexes, with Fo and Pi or with Fo and GDP-from Methanosarcina mazei. The active site is located at the C-terminal end of a Rossmann-fold core, and three large insertions make significant contributions to the active site and dimer formation. The observed binding modes of Fo and GDP can explain known biochemical properties of CofD, and are also supported by our binding assays. The structures provide significant molecular insights into the biosynthesis of the F420 coenzyme. Large structural differences in the active site region of the non-F420-producing CofD homologs suggest that they catalyze a different biochemical reaction.

About this StructureAbout this Structure

3C3D is a Single protein structure of sequence from Methanosarcina mazei go1. Full crystallographic information is available from OCA.

ReferenceReference

Molecular insights into the biosynthesis of the F420 coenzyme., Forouhar F, Abashidze M, Xu H, Grochowski LL, Seetharaman J, Hussain M, Kuzin A, Chen Y, Zhou W, Xiao R, Acton TB, Montelione GT, Galinier A, White RH, Tong L, J Biol Chem. 2008 Feb 5;. PMID:18252724

Page seeded by OCA on Thu Mar 20 19:02:23 2008

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OCA

@@ Line 1: / Line 1: @@
-[[Image:3c3d.jpg|left|200px]]<br /><applet load="3c3d" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:3c3d.jpg|left|200px]]
-caption="3c3d, resolution 2.50&Aring;" />
-'''Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and phosphate. Northeast Structural Genomics Target MaR46'''<br />
+ {{Structure
+|PDB= 3c3d |SIZE=350|CAPTION= <scene name='initialview01'>3c3d</scene>, resolution 2.50&Aring;
+|SITE= <scene name='pdbsite=AC1:Po4+Binding+Site+For+Residue+A+402'>AC1</scene>, <scene name='pdbsite=AC2:Po4+Binding+Site+For+Residue+B+402'>AC2</scene>, <scene name='pdbsite=AC3:Po4+Binding+Site+For+Residue+C+402'>AC3</scene>, <scene name='pdbsite=AC4:Po4+Binding+Site+For+Residue+D+402'>AC4</scene>, <scene name='pdbsite=AC5:Fo1+Binding+Site+For+Residue+A+401'>AC5</scene>, <scene name='pdbsite=AC6:Fo1+Binding+Site+For+Residue+B+401'>AC6</scene>, <scene name='pdbsite=AC7:Fo1+Binding+Site+For+Residue+C+401'>AC7</scene> and <scene name='pdbsite=AC8:Fo1+Binding+Site+For+Residue+D+401'>AC8</scene>
+|LIGAND= <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene> and <scene name='pdbligand=FO1:'>FO1</scene>
+|ACTIVITY=
+|GENE= cofD, MM_1874 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=192952 Methanosarcina mazei Go1])
+}}
+'''Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and phosphate. Northeast Structural Genomics Consortium target MaR46'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-C3D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanosarcina_mazei_go1 Methanosarcina mazei go1] with <scene name='pdbligand=PO4:'>PO4</scene> and <scene name='pdbligand=FO1:'>FO1</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Sites: <scene name='pdbsite=AC1:Po4+Binding+Site+For+Residue+A+402'>AC1</scene>, <scene name='pdbsite=AC2:Po4+Binding+Site+For+Residue+B+402'>AC2</scene>, <scene name='pdbsite=AC3:Po4+Binding+Site+For+Residue+C+402'>AC3</scene>, <scene name='pdbsite=AC4:Po4+Binding+Site+For+Residue+D+402'>AC4</scene>, <scene name='pdbsite=AC5:Fo1+Binding+Site+For+Residue+A+401'>AC5</scene>, <scene name='pdbsite=AC6:Fo1+Binding+Site+For+Residue+B+401'>AC6</scene>, <scene name='pdbsite=AC7:Fo1+Binding+Site+For+Residue+C+401'>AC7</scene> and <scene name='pdbsite=AC8:Fo1+Binding+Site+For+Residue+D+401'>AC8</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C3D OCA].
+C3D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanosarcina_mazei_go1 Methanosarcina mazei go1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C3D OCA].
 ==Reference==
-Molecular insights into the biosynthesis of the F420 coenzyme., Forouhar F, Abashidze M, Xu H, Grochowski LL, Seetharaman J, Hussain M, Kuzin A, Chen Y, Zhou W, Xiao R, Acton TB, Montelione GT, Galinier A, White RH, Tong L, J Biol Chem. 2008 Feb 5;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18252724 18252724]
+Molecular insights into the biosynthesis of the F420 coenzyme., Forouhar F, Abashidze M, Xu H, Grochowski LL, Seetharaman J, Hussain M, Kuzin A, Chen Y, Zhou W, Xiao R, Acton TB, Montelione GT, Galinier A, White RH, Tong L, J Biol Chem. 2008 Feb 5;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18252724 18252724]
 [[Category: Methanosarcina mazei go1]]
 [[Category: Single protein]]
@@ Line 37: / Line 46: @@
 [[Category: protein structure initiative]]
 [[Category: psi-2]]
-[[Category: structural genomics]]
+[[Category: structural genomic]]
 [[Category: transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:08:20 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:02:23 2008''