3c3d: Difference between revisions

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[[Image:3c3d.png|left|200px]]
==Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and phosphate. Northeast Structural Genomics Consortium target MaR46==
<StructureSection load='3c3d' size='340' side='right' caption='[[3c3d]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3c3d]] is a 4 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C3D FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FO1:1-DEOXY-1-(8-HYDROXY-2,4-DIOXO-3,4-DIHYDROPYRIMIDO[4,5-B]QUINOLIN-10(2H)-YL)-D-RIBITOL'>FO1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3cgw|3cgw]], [[3c3e|3c3e]]</td></tr>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cofD, MM_1874 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=192952 Methanosarcina mazei Go1])</td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3c3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c3d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c3d RCSB], [http://www.ebi.ac.uk/pdbsum/3c3d PDBsum], [http://www.topsan.org/Proteins/NESGC/3c3d TOPSAN]</span></td></tr>
<table>
== 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/c3/3c3d_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <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].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Coenzyme F(420), a hydride carrier, is found in Archaea and some bacteria and has crucial roles in methanogenesis, antibiotic biosynthesis, DNA repair, and activation of antitubercular compounds. CofD, 2-phospho-l-lactate transferase, catalyzes the last step in the biosynthesis of F(420)-0 (F(420) without polyglutamate), by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (Fo). CofD is highly conserved among F(420)-producing organisms, and weak sequence homologs are also found in non-F(420)-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 P(i) 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 F(420) coenzyme. Large structural differences in the active site region of the non-F(420)-producing CofD homologs suggest that they catalyze a different biochemical reaction.


{{STRUCTURE_3c3d|  PDB=3c3d  |  SCENE=  }}
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 Apr 25;283(17):11832-40. Epub 2008 Feb 5. PMID:18252724<ref>PMID:18252724</ref>


===Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and phosphate. Northeast Structural Genomics Consortium target MaR46===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_18252724}}
== References ==
 
<references/>
==About this Structure==
__TOC__
[[3c3d]] is a 4 chain structure with 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].
</StructureSection>
 
==Reference==
<ref group="xtra">PMID:018252724</ref><references group="xtra"/>
[[Category: Methanosarcina mazei go1]]
[[Category: Methanosarcina mazei go1]]
[[Category: Abashidze, M.]]
[[Category: Abashidze, M.]]

Revision as of 00:00, 3 October 2014

Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and phosphate. Northeast Structural Genomics Consortium target MaR46Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and phosphate. Northeast Structural Genomics Consortium target MaR46

Structural highlights

3c3d is a 4 chain structure with sequence from Methanosarcina mazei go1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
NonStd Res:
Related:3cgw, 3c3e
Gene:cofD, MM_1874 (Methanosarcina mazei Go1)
Resources:FirstGlance, OCA, RCSB, PDBsum, TOPSAN

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

Coenzyme F(420), a hydride carrier, is found in Archaea and some bacteria and has crucial roles in methanogenesis, antibiotic biosynthesis, DNA repair, and activation of antitubercular compounds. CofD, 2-phospho-l-lactate transferase, catalyzes the last step in the biosynthesis of F(420)-0 (F(420) without polyglutamate), by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (Fo). CofD is highly conserved among F(420)-producing organisms, and weak sequence homologs are also found in non-F(420)-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 P(i) 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 F(420) coenzyme. Large structural differences in the active site region of the non-F(420)-producing CofD homologs suggest that they catalyze a different biochemical reaction.

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 Apr 25;283(17):11832-40. Epub 2008 Feb 5. PMID:18252724[1]

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

References

  1. ↑ 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. Molecular insights into the biosynthesis of the F420 coenzyme. J Biol Chem. 2008 Apr 25;283(17):11832-40. Epub 2008 Feb 5. PMID:18252724 doi:10.1074/jbc.M710352200

3c3d, resolution 2.50Å

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